CN104603287B - Method for determining nucleotide sequence - Google Patents

Method for determining nucleotide sequence Download PDF

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CN104603287B
CN104603287B CN201380037100.5A CN201380037100A CN104603287B CN 104603287 B CN104603287 B CN 104603287B CN 201380037100 A CN201380037100 A CN 201380037100A CN 104603287 B CN104603287 B CN 104603287B
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primer
target
seq
nucleic acid
sequencing
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CN104603287A (en
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安东尼·约翰·亚弗拉特
李龙飞
郑宗立
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General Hospital Corp
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Abstract

The techniques described herein by being enriched with target sequence before sequence is sequenced for for example determining the method for oligonucleotide sequence.

Description

Method for determining nucleotide sequence
The cross reference of related application
According to 35U.S.C. § 119 (e), the U.S. Provisional Application No. 61/ submitted this application claims on May 10th, 2012 The priority for the U.S. Provisional Application No. 61/679,302 that 645,364 and 2012 on Augusts are submitted for 3, by reference by it Content is fully incorporated herein.
Sequence table
The application includes sequence table, and the sequence table is submitted in ascii by EFS-Web, and with the side of reference Formula is fully incorporated herein.The ASCII copies created on March 8th, 2013, were named as 030258-074962-PCT_ SL.txt, the byte of size 41,722.
Governmental support
The present invention is in the base authorized by NIH (National Institutes of Health) Completed under gold 5R21CA161590 federal funding.U.S. government has certain rights in the invention.
Technical field
The techniques described herein are related to the method for measure oligonucleotide sequence.
Background technology
It is sequenced compared to full-length genome, full extron group and full transcript profile, next generation's sequencing (next-generation Sequencing the target enrichment before) is more cost effective, therefore is more suitable for finding in research and being widely implemented in clinical practice.Example Such as, the high overburden depth (high coverage depth) provided by target enrichment method can realize compared with wide dynamic range etc. Position gene count (in gene expression and copy number are assessed) and the detection being mutated to low frequency are (thin for evaluating the body in cancer The key feature that cytoplasmic process becomes).Example currently used for the enrichment strategy of next generation's sequencing includes：Capture analysis based on hybridization (TruSeq Capture, Illumina；SureSelect Hybrid Capture, Agilent) and based on polymerase chain reaction Answer analysis (HaloPlex, the Agilent of (PCR)；AmpliSeq, Ion Torrent；TruSeq Amplicon, Illumina； Emulsion/digital pcr, Raindance).Method based on hybridization not only captures the targeting sequence of captured probe covering, also catches The base of missing the target (near off-target bases) near consumption sequencing ability is received.In addition, these methods all compare Time-consuming, labour intensive and specificity levels are relatively low.The method of PCR-based amplification more simply and faster, but is set according to conventional Meter needs to use the forward primer and reverse primer positioned at target gene seat both wings.Especially, there is unknown fusion companion for detection For the genome rearrangement (genomic rearrangements) of companion (fusion partner), PCR is inapplicable.
The content of the invention
Method of the techniques described herein for measure oligonucleotide sequence.In some embodiments, it is as described herein Method is related to be enriched with before sequence is sequenced to target sequence.
In one aspect, the techniques described herein are related to measure and known target nucleotide sequences adjoining (contiguous To the method for nucleotide sequence), methods described include：(a) by the target nucleic acid comprising known target nucleotide sequences and general widow Nucleotides pigtail connection (adaptor) connects；(b) target nucleic acid is expanded with the first adapter-primer and the first target specific primer A part and the general oligonucleotide pigtail connection amplification chain；(c) drawn with the second adapter-primer and the second target-specific A part for thing amplification amplicon as caused by step (b)；(d) using the first sequencing primer and the second sequencing primer to by step (c) amplification part is sequenced caused by；Wherein, the general oligonucleotide pigtail connection, which includes first, can connect duplex ends With the second unpaired end；Wherein, the general oligonucleotide pigtail connection includes sealed joint (blocking strand) and expanded Chain (amplification strand)；Wherein, the sealed joint includes 5 ' double stranded sections；Wherein, the amplification chain includes Unpaired 5 ' part, 3 ' double stranded sections and 3 ' T protrude (overhang)；Wherein, the amplification chain includes and the first sequencing primer With the second sequencing primer identical nucleotide sequence；Wherein, the sealed joint and it is described amplification chain double stranded section substantially (substantially) it is complementary, and formation can connect duplex ends comprising 3 ' T are protruded first；Wherein, the double stranded section foot It is enough long, to maintain double chain form at a temperature of connection；Wherein, include can be special at an annealing temperature for first target specific primer The opposite sex is annealed to the nucleotide sequence of the known target nucleotide sequences of the target nucleic acid；Wherein, the second target specific primer bag Containing 3 ' partly with 5 ' parts, described 3 ' partly containing can specificity be annealed to what the amplicon as caused by step (b) was included The nucleotide sequence of a part for known target nucleotide sequences, described 5 ' partly contain and the second sequencing primer identical nucleic acid sequence Row, and second target specific primer is nested (nested) relative to first target specific primer；Wherein, described One adapter-primer includes 5 ' the part identical nucleotide sequences with first sequencing primer；And wherein, second joint Primer includes a part of identical nucleotide sequence with first sequencing primer, and embedding relative to first adapter-primer Set.
In some embodiments, the sealed joint of general oligonucleotide pigtail connection can further include 3 ' unpaired portions Point, 3 ' the unpaired part substantially not with expand chain 5 ' unpaired partial complementarities；And wherein, the 3 ' of sealed joint does not match somebody with somebody To partly substantially not with any Primers complementary, or being substantially different from any primer.In some embodiments, the second joint Primer can be nested relative to the first adapter-primer by least three nucleotides.In some embodiments, containing with first sequencing The part of the amplification chain of primer and the second sequencing primer identical nucleotide sequence can at least partly be contained in 5 ' not matching somebody with somebody for amplification chain To in part.
In some embodiments, the first target specific primer can further include 5 ' sequence label parts, the 5 ' mark Label Sequence is included substantially not with any other partial complementarity of any primer or being substantially different from appointing for any primer The nucleotide sequence of the high GC content of what other parts.In some embodiments, the first target specific primer can further include 5 ' sequence label parts, the 5 ' sequence label be partially contained under annealing temperature will not specificity be annealed to any primer or its The nucleotide sequence of the high GC content of any other part of complement.In some embodiments, the second adapter-primer can with it is complete Long first sequencing primer is identical.In some embodiments, the part of the specific target specific primer for being annealed to known target can The specificity annealing at a temperature of about 65 DEG C in PCR buffer solutions.
In some embodiments, methods described further can comprise the following steps before step (a)：Nucleic acid is carried out Mechanical shearing；Repair the nucleic acid experience end；Make the nucleic acid experience phosphorylation；And make the nucleic acid experience adenylate Change.In some embodiments, sample may include genomic DNA.In some embodiments, sample may include RNA, and institute The method of stating can further comprise making the sample experience reverse transcriptase scheme (reverse transcriptase regimen) First step.In some embodiments, the reverse transcriptase scheme may include to use random hexamer (random hexamers)。
In embodiments, it is known that target sequence may be included in gene rearrangement (gene rearrangement). In some embodiments, gene rearrangement may be present in the nucleic acid in the group being made up of following nucleic acid：Genome DNA, RNA and cDNA.In some embodiments, gene rearrangement can include oncogene (oncogene).In some embodiments In, gene rearrangement can include fusion oncogene.
In some embodiments, nucleic acid product can be sequenced by PCR sequencing PCR of future generation.In some embodiments In, PCR sequencing PCR of future generation may include the method in the group being made up of following methods：Ion Torrent、Illumina、 SOLiD, 454, extensive parallel signature sequencing (Massively Parallel Signature Sequencing), solid phase can Inverse Dye Terminator thing sequencing (reversible dye-terminator sequencing) and DNA nanospheres sequencing (DNA nanoball sequencing).In some embodiments, under selected by the first sequencing primer and the second sequencing primer compatibility Generation PCR sequencing PCR.
In some embodiments, methods described may include the unitary part of sample or sample and multigroup first target is special Property primer and the second target specific primer contact.In some embodiments, methods described may include comprising the single of sample Reactant mixture contacts with multigroup first target specific primer and the second target specific primer.In some embodiments, it is multigroup First target specific primer and the second target specific primer specific can be annealed to the known target nucleus glycosides included by different genes Acid sequence.In some embodiments, at least two group of first target specific primer and the second target specific primer can specificity move back The fiery different piece to known target nucleotide sequences.In some embodiments, at least two group of first target specific primer and Two target specific primers specific can be annealed to the different piece of the individual gene containing known target nucleotide sequences.In some realities Apply in mode, at least two group of first target specific primer and the second target specific primer can specificity be annealed to containing known target nucleus The different extrons of the gene of nucleotide sequence.In some embodiments, multiple first target specific primers can include identical 5 ' sequence label parts.In some embodiments, general oligonucleotide pigtail connection can further include bar code part (barcode portion).In some embodiments, can by several samples each with unique (unique) barcode section The general oligonucleotide pigtail connection contact divided, wherein, the sample is merged into (pooled) after step (a).
In some embodiments, each amplification step may include PCR amplification side of the length for -20 circulations of 5 circulations Case circulation group.In some embodiments, target specific primer and adapter-primer can be designed to the annealing temperature at about 61-72 DEG C Degree is lower specific to be annealed to their complementary series.In some embodiments, can be by target specific primer and adapter-primer It is designed to that under about 65 DEG C of annealing temperature specific their complementary series can be annealed to.
In some embodiments, sample may include the biological sample for being derived from subject.In some embodiments, sample Product are available from needing the subject for treating the disease related to hereditary change (genetic alteration).In some implementations In mode, disease can be cancer.In some embodiments, sample may include tumor cell group.In some embodiments, sample Product may include that tumor biopsies cut into slices (biopsy).In some embodiments, cancer can be lung cancer.
In embodiments, it is known that target sequence may be included in disease related gene.In some embodiments, Know that target sequence may be included in the gene rearrangement product in sample.In some embodiments, gene rearrangement product can be cancer base Cause.
In embodiments, it is known that target sequence can include the sequence of the gene in the group selected from following gene： ALK, ROS1 and RET.In some embodiments, at least one set of first target specific primer and the second target specific primer are optional From in the group being made up of following primer：SEQ ID NO：5 and SEQ ID NO：6；SEQ ID NO：7 and SEQ ID NO：8； SEQ ID NO：9 and SEQ ID NO：10；SEQ ID NO：11 and SEQ ID NO：12；SEQ ID NO：13 and SEQ ID NO： 14；SEQ ID NO：15 and SEQ ID NO：16；SEQ ID NO：17 and SEQ ID NO：18；SEQ ID NO：19 and SEQ ID NO：20；SEQ ID NO：21 and SEQ ID NO：22；SEQ ID NO：23 and SEQ ID NO：24；SEQ ID NO：25 and SEQ ID NO：26；SEQ ID NO：27 and SEQ ID NO：28；SEQ ID NO：29 and SEQ ID NO：30；SEQ ID NO：31 Hes SEQ ID NO：32；SEQ ID NO：33 and SEQ ID NO：34；SEQ ID NO：35 and SEQ ID NO：36；And SEQ ID NO：37 and SEQ ID NO：38.
In some embodiments, in the sample obtained from the tumour of subject, the presence of ALK gene rearrangement can be said Bright tumour is easily influenceed by the treatment carried out with the therapeutic agent in the group by following material composition：ALK inhibitor, gram azoles For Buddhist nun (crizotinib) (PF-02341066), AP26113, LDK378,3-39, AF802, IPI-504, ASP3026, AP- 26113rd, X-396, GSK-1838705A, CH5424802 and NVP-TAE684.
In some embodiments, in the sample obtained from the tumour of subject, the presence of ROS1 gene rearrangement can Illustrate that tumour is easily influenceed by the treatment carried out with the therapeutic agent in the group by following material composition：ROS inhibitor, ALK inhibitor, gram azoles are for Buddhist nun (PF-02341066), AP26113, LDK378,3-39, AF802, IPI-504, ASP3026, AP- 26113rd, X-396, GSK-1838705A, CH5424802 and NVP-TAE684.
In some embodiments, in the sample obtained from the tumour of subject, the presence of RET gene rearrangement can be said Bright tumour is easily influenceed by the treatment carried out with the therapeutic agent in the group by following material composition：RET inhibitor, DP- 2490th, DP-3636, SU5416, BAY 43-9006, BAY 73-4506 (Rui Gefeini, regorafenib), ZD6474, NVP- AST487, Sorafenib (sorafenib), RPI-1, XL184, ZD6474 (vandetanib), Sutent (sunitinib), Imatinib (imatinib), pazopanib (pazopanib), Axitinib (axitinib), Mo Tesai Buddhist nun (motesanib), Gefitinib (gefitinib) and withaferin A (withaferin A).
In one aspect, the techniques described herein are related to the method for the treatment of cancer, and methods described includes：According to described herein Method, the presence reset to being derived from more than one oncogenes in the tumor sample for the subject for needing treating cancer examines Survey；Give the effective treatment of cancer of tumour for being reset with any oncogene detected.In some embodiments, select Can be effective for the tumour reset with ALK oncogenes from the therapeutic agent in the group by following material composition：ALK inhibitor, Gram azoles is for Buddhist nun (PF-02341066), AP26113, LDK378,3-39, AF802, IPI-504, ASP3026, AP-26113, X- 396th, GSK-1838705A, CH5424802 and NVP-TAE684.In some embodiments, selected from by following material group Into group in therapeutic agent can be effective for the tumour reset with ROS1 oncogenes：ROS1 inhibitor, ALK inhibitor, gram azoles For Buddhist nun (PF-02341066), AP26113, LDK378,3-39, AF802, IPI-504, ASP3026, AP-26113, X-396, GSK-1838705A, CH5424802 and NVP-TAE684.In some embodiments, selected from by following material composition Therapeutic agent in group can be effective for the tumour reset with RET oncogenes：RET inhibitor, DP-2490, DP-3636, SU5416, BAY 43-9006, BAY 73-4506 (Rui Gefeini), ZD6474, NVP-AST487, Sorafenib, RPI-1, XL184, ZD6474, Sutent, Imatinib, pazopanib, Axitinib, Mo Tesaini, Gefitinib and liquor-saturated eggplant Plain A.
In one aspect, whether the techniques described herein are related to measure needs the subject for the treatment of cancer can be to given treatment The method to respond, methods described include：According to method described herein, to being derived from cancer base in the tumor sample of subject Because the presence of rearrangement is detected；Wherein, if detecting the presence of oncogene rearrangement, determine the subject to targetting oncogene The treatment of rearrangement product responds.
In some embodiments, when detecting the presence of the rearrangement of ALK oncogenes, subject can be to selected from by following thing Therapeutic agent in the group that matter is formed responds：ALK inhibitor, gram azoles for Buddhist nun (PF-02341066), AP26113, LDK378,3-39, AF802, IPI-504, ASP3026, AP-26113, X-396, GSK-1838705A, CH5424802 and NVP-TAE684.In some embodiments, when detecting the presence of the rearrangement of ROS1 oncogenes, subject can be to selected from by such as Therapeutic agent in the group that lower material is formed responds：ALK inhibitor, gram azoles for Buddhist nun (PF-02341066), AP26113, LDK378,3-39, AF802, IPI-504, ASP3026, AP-26113, X-396, GSK-1838705A, CH5424802 and NVP-TAE684。
In some embodiments, when detecting the presence of the rearrangement of RET oncogenes, subject can be to selected from by following thing Therapeutic agent in the group that matter is formed responds：RET inhibitor, DP-2490, DP-3636, SU5416, BAY 43-9006, BAY 73-4506 (Rui Gefeini), ZD6474, NVP-AST487, Sorafenib, RPI-1, XL184, ZD6474, Buddhist nun of relaxing replace Buddhist nun, Imatinib, pazopanib, Axitinib, Mo Tesaini, Gefitinib and withaferin A.
In some embodiments, cancer can be lung cancer.
Brief description of the drawings
Fig. 1 depicts illustrating for the library construction example of targeted rna and DNA sequencing.1) use and come from FFPE The total nucleic acid of sample is as parent material, the standardization program synthesized using double-strand cDNA.Or parent material is alternatively shearing gDNA.2) after purifying (cleanup), make the end reparation of double-strand cDNA or gDNA experience and dA tailings, be then directly connected to half Short (half-truncated) Y-shaped connector, need not be purified therebetween.3) SPRI after purification, uses multiple gene specific primer (GSP1) sample of connection and the 20-mer (A20) of Ion Torrent short length forward primers A 5 ', is made with 65 DEG C of annealing temperature The PCR amplifications of 14 circulations of experience.4) the 2nd SPRI after purification, using being marked with Ion Torrent reverse primers (P1_GSP2) Multinest gene-specific primer (GSP1 3 ' downstreams and in same direction) and forward primer A (total length 30-mer), with 65 DEG C of annealing temperature subjects the sample to the PCR amplifications of 14 other circulations.5) after purification, product is the 3rd last SPRI It is ready for the Ion Torrent libraries of downstream emulsion-based PCR and sequencing.Sample merging can be carried out after step 2.
Fig. 2 depicts mapping (mapping) result, it was demonstrated that in the operating different primers of sequencing of ROS1 sequences (point) extension products, the result are included corresponding to genomic DNA (across intron-exon border), cDNA (across extron) With fusion cDNA (on extron 34, the mapping on fusion partner SLC34A2 is not shown here) read (reads).Reach To 91.8% specificity (127,446/138,787).
Fig. 3 A depict the diagrammatic illustration of nested primers targeting strategy by taking ROS1 as an example.On ROS1, ALK and RET, analysis Target group (assay target panel) includes 17 couples of GSP1 and GSP2 altogether.Fig. 3 B are depicted using gDNA and cDNA templates The possibility type of representative extension products.
Fig. 4 A depict to be mapped using Integrative Genomics Viewer visualization read.Fig. 4 B are depicted The sequence of two alternative splicing fusion sequences.Fig. 4 C depict the involved gene of report and (are annotated with extron, reading frame and melt Close read coverage details) in fusion transcript conclusive table.
Fig. 5 depicts the result of exemplary sequencing operation.
Fig. 6 and Fig. 7 respectively depict the example of the sequencing operation result of ALK sequences and RET sequences.
Fig. 8 depicts the diagrammatic illustration of targeting sequence measurement as described herein.
Fig. 9 depicts the schematic diagram of illustrative general oligonucleotide pigtail connection.
Embodiment
The embodiment of technology described herein is related to the method for being measured and (that is, being sequenced) to oligonucleotide sequence.One In a little embodiments, method described herein is related to the method that target sequence is enriched with before sequencing steps.In some embodiments, Before sequencing steps, the sequence of an end of target sequence to be enriched with is unknown.
For convenience, provided hereinafter some terms used in specification, embodiment and appended claims With the implication of phrase.Unless otherwise stated or implied in some context, following term and phrase include provided below contain Justice.The definition is provided to aid in describing embodiment, and by the scope of the present invention is only limited by claim, therefore It is not intended to limit claimed invention.Unless otherwise defined, all technical terms used herein and section are academic Language has the identical implication being generally understood with the ordinary technical staff in the technical field of the invention.If in this area Exist between the use of middle term and term provided in this article definition it is obvious inconsistent, should be to determine provided in this specification Justice is defined.
For convenience, some terms used in specification, embodiment and appended claims are have collected at this.
Terms used herein " reducing (decrease) ", " reducing (reduced/reduction) " " suppress (inhibit) it " generally can mean that the reduction of statistically significant amount.However, to avoid doubt, " (reduced/ is reduced Reduction) ", " reduce (decrease) " or " suppressing (inhibit) " represents to reduce at least 10% compared to reference level, example Such as reduction at least about 20% or at least about 30% or at least about 40% or at least about 50% or at least about 60% or at least about 70% or at least about 80% or at least about 90% or up to and including reducing by 100% (e.g., compared to the missing water of reference sample Flat or undetectable level) or compared to reference level reduce any amount between 10% to 100%.In mark (marker) or in the case of symptom (symptom), it is meant that this horizontal statistically significant reduction.For example, the reduction It can be at least 10%, at least 20%, at least 30%, at least 40% or more, and be preferably dropped to be considered as to be not suffering from such a illness Individual normal range (NR) in level.
Terms used herein " increase (increased/increase) ", " enhancing (enhance) " or " activation (activate) it " generally can mean that the increase of statistically significant amount；To avoid doubt, term " increase (increased/ Increase) ", " enhancing (enhance) " or " activation (activate) " is represented compared to reference level's increase at least 10%, such as Increase at least about 20% or at least about 30% or at least about 40% or at least about 50% or at least about 60% or at least about 70% or at least about 80% or at least about 90% or up to and including increase by 100% or compared to reference level increase 10% Any amount between to 100%；Or compared at least about 2 times or at least about 3 times of reference level or at least about 4 times or at least about 5 Times or at least about 10 times of increase or the increase of any amount between 2 times and 10 times or a greater amount of increases.
Term as used herein " subject " refers to human or animal.Generally, the animal is vertebrate, such as primate Animal, rodent, domestic animal or hunting animal (game animal).Primate includes chimpanzee, machin, Ateles With macaque (such as rhesus macaque).Rodent includes mouse, rat, marmot (woodchucks), ferret (ferrets), rabbit and storehouse Mouse.Domestic animal and hunting animal include ox (cows), horse, pig, deer, wild ox, buffalo, feline species (e.g., domestic cat), Canidae species (e.g., dog, fox, wolf), birds species (e.g., chicken, emu (emu), ostrich) and fish (e.g., trout (trout), catfish and salmon Fish).In some embodiments, subject is mammal, for example, primate, such as mankind.Term " individual ", " suffer from Person " and " subject " are used interchangeably herein.
Preferably, subject is mammal.The mammal can be people, non-human primate, mouse, rat, Dog, cat, horse or ox, but it is not limited to these examples.Mammal in addition to people can be advantageously used as representing such as lung cancer animal The subject of model.Subject can be male or female.
Subject can be previously to be diagnosed with or be accredited as by or with needing the illness treated (for example, cancer Disease) or more than one complication related to such a illness subject, and the subject has optionally received to the disease Disease or the treatment of more than one complication related to the illness.Or subject can also be previously not to be diagnosed as suffering from There is the subject of the illness (for example, cancer) or more than one complication related to the illness.For example, subject can be The subject of more than one risk factors for the illness or more than one complication related to the illness is shown, Or can be the subject for not showing risk factors.
Treatment " subject in need " for particular condition can be with the illness, be diagnosed as with the illness, Or the subject in the risk for developing into the illness.
" disease related to hereditary change " used herein refer at least partly by relative to healthy wild type by Any disease caused by the change (for example, deletion, insertion, SNP, gene rearrangement) of the inhereditary material of subject for examination person.Such as Fruit changes that increase subject develops into the risk of disease, increase subject (including communicable disease or has infectiousness to disease The disease of component) neurological susceptibility, cause the generation of disease associated molecule or make cell be changed into it is ill or abnormal (for example, The missing of cell cycle regulating in cancer cell), disease at least partly can be caused by the change in subject's inhereditary material.Disease Disease can be related to a variety of hereditary changes, for example, cancer.
Term as used herein " nucleic acid " or " nucleotide sequence " refer to comprising ribonucleic acid, DNA or its is similar Any molecule, the preferred polymeric molecule of thing unit.The nucleic acid can be single-stranded or double-strand.Single-chain nucleic acid can be denaturation double-strand The nucleic acid of a DNA chain.Or single-chain nucleic acid can be the single-chain nucleic acid for not deriving from any double-stranded DNA.In one aspect, Template nucleic acid is DNA.On the other hand, template RNA.Suitable nucleic acid molecules are DNA, including genomic DNA or cDNA.Its Its suitable nucleic acid molecules is RNA, including mRNA.
In the case of nucleic acids, term as used herein " separation " or " partially purified " are related to from natural next at it The nucleic acid isolated in source together with nucleic acid in existing at least one other composition (for example, nucleic acid or polypeptide)；And/or from work as The core that can be isolated when being expressed by cell together with nucleic acid in existing at least one other composition (for example, nucleic acid or polypeptide) Acid.The nucleic acid of chemical synthesis or the nucleic acid synthesized using in-vitro transcription/translation are considered as " separation ".
Term " gene " refer to transcribe in vitro or in vivo when being operably coupled to appropriate regulatory sequences (DNA) into RNA nucleotide sequence.The gene may include the regulatory region before and after encoding gene, for example, 5 ' untranslateds (5 ' UTR) Sequence or " leading (leader) " sequence；And 3 ' UTR or " trail (trailer) " sequence；And respectively encode fragment and (show outside Son) between intervening sequence (intervening sequences) (introne).
The hydrogen bond base that term as used herein " complementation " is related between nucleotide base G, A, T, C and U matches to be formed The hierarchy (hierarchy) of preference, during so that proper two kinds given polynucleotides or polynucleotide sequence annealing with one another, A and T pairings, G and C are matched in DNA, and G and C pairings, A and U are matched in RNA." being substantially complementary " used herein refers to Nucleic acid molecules or part thereof (for example, primer) have at least in the total length of the molecule or part thereof with the second nucleotide sequence 90% complementarity, for example, 90% is complementary, 95% complementary, 98% complementary, 99% complementary or 100% complementation.It is used herein " substantially the same " refers to nucleic acid molecules or part thereof to be had in the total length of the molecule or part thereof with the second nucleotide sequence At least 90% uniformity, for example, 90% is consistent, 95% consistent, 98% consistent, 99% consistent or 100% is consistent.
In the case where specificity is for the primer of target nucleic acid, used herein " special " guide between thing and target Complementarity it is horizontal, it is such it is complementary it is horizontal to exist as annealing temperature：In the annealing temperature, primer will anneal To the target nucleic acid and mediate the amplification of the target nucleic acid and be not annealed to the non-target sequences in sample or mediation sample in The amplification of non-target sequences.
" amplified production (amplified product/amplification product) " used herein or " expand Increase sub (amplicon) " refer to the oligonucleotides as caused by reacting PCR, the oligonucleotides be specific target nucleic acid template chain and/ Or the copy of a part for its complementary series, its on nucleotide sequence correspond to the template oligonucleotide sequence and/or its Complementary series.Amplified production, which can further include, has specific sequence to primer and (it is the target nucleic acid positioned at sequence And/or a part for its complement) both sides sequence.Although may be referred to its single chain, amplified production as described herein is usual It will be double-stranded DNA.
" part (portion) " of nucleic acid molecules used herein refers to the continuous nucleotide collection included by the molecule (contiguous set of nucleotides).Part can include the completely or only subset of the nucleotides included by the molecule. Part can be double-strand or single-stranded.
Term as used herein " treatment (treat/treatment/treating) " " improves (amelioration) " refer to treatment handle, wherein, it is therefore an objective to reverse, mitigate, improving, suppressing, be slowed or shut off with disease or The progress or the order of severity of disorderly (for example, lung cancer) related illness.Term " treatment " includes reducing or mitigating illness and illness Relevant disease or at least one harmful effect or the symptom of disorder.If one or more symptoms or clinical marker thing are subtracted Few, then treatment is typically " effective ".Or if progression of disease is reduced or stopped, treatment is " effective ".Also To say, " treatment " not only includes improvement of symptom or mark, compared with also including situation desired when not obtaining medical treatment and Speech symptom progress or the termination deteriorated at least delay.Beneficial or desired clinical effectiveness includes but is not limited to：Mitigate a kind of Or a variety of symptoms, disease degree is reduced, (that is, do not deteriorate) morbid state stably, postpone or delay progression of disease, improvement or mitigation (palliation) morbid state, alleviation (part or all of), and/or the reduction death rate, no matter the above results are detectable It is or undetectable.Term " treatment " disease also includes the symptom for providing disease or dysgenic releive (including is appeased and controlled Treat (palliative treatment)).
Term " statistically significant (statistically significant) " or " significantly (significantly) " refer to statistical significance, and generally mean that less than normal two standard deviations (2SD) of marker concentration It is or lower.
Except in embodiment is operated or place indicated otherwise, the amount of expression composition used herein or reaction condition Whole numerical value all should be understood that in all cases to be modified by term " about ".Being connected the term " about " used with percentage can Mean ± 1%.
Term as used herein " include/including (comprising or comprises) " is used to represent to method or group The necessary composition of compound, method and its respective part, and it is regardless of whether necessary all still to unspecified key element Keep opening.
Term " Consists of " is related to composition, method and its respective part as described herein, and exclusion does not exist Any key element being described in detail in embodiment description.
Term as used herein "consisting essentially of ..." is related to those required to given embodiment element.The term Allow the basis for not influenceing the embodiment substantially and the element of novelty or the feature to work be present.
Unless clearly being referred else in context, singular references " one (a/an) " and " being somebody's turn to do/(the) " cover plural number Signified thing.Similarly, unless clearly being referred else in context, word " or (or) " is intended to " and (and) ".Although Similar or equivalent method and material can be used in practice or test disclosed herein with method described herein and material, close Suitable method and material is described below.Abridge " e.g. " such as (exempli gratia) from Latin, and It is used to represent non-limiting examples herein.Therefore, abbreviation " e.g. " is synonymous with term " such as (for example) ".
The definition of Essential Terms can be found in following works in Celluar and Molecular Biology：“The Merck Manual of Diagnosis and Therapy ", the 19th edition, Merck Research Laboratories are published, and 2006 (ISBN 0-911910-19-0)；Robert S.Porter etc. (work), The Encyclopedia of Molecular Biology, Blackwell Science Ltd. are published, 1994 (ISBN 0-632-02182-9).Commonly used in molecular biology The definition of term can also be found in following works：Benjamin Lewin, Genes X, Jones＆Bartlett Publishing is published, 2009 (ISBN-10:0763766321)；Kendrew etc. (work), Molecular Biology and Biotechnology:A Comprehensive Desk Reference, VCH Publishers, Inc. publication, 1995 (ISBN 1-56081-569-8)；And Current Protocols in Protein Sciences 2009, Wiley Intersciences, Coligan etc. write.
Unless otherwise indicated, the present invention is carried out using the standardization program described in for example following works：Sambrook etc., Molecular Cloning:A Laboratory Manual (third edition), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., USA (2001)；And Davis etc., Basic Methods in Molecular Biology, Elsevier Science Publishing, Inc., New York, USA (1995), to quote Mode its entirety is fully incorporated herein.
Other terms are defined in the description of various aspects of the present invention.
As described herein is measure and the method for the nucleotide sequence of known target nucleotide sequences adjoining.Traditional sequencing methods It is randomly generated sequence information (for example, " air gun " be sequenced), or the sequence information between two known arrays for designing primer. On the contrary, in some embodiments, method described herein allows with high specific level and high sensitivity level to known sequence The upstream in single region or the nucleotide sequence in downstream of row are measured (for example, sequencing).
In some embodiments, method described herein is related to using sequencing technologies of future generation measure nucleotide sequence The method of specific nucleotide sequence is enriched with before.In some embodiments, it is described enrichment specific nucleotide sequence method simultaneously Hybridization enrichment is not included.
In some embodiments, the techniques described herein can relate to measure and the nucleosides of known target nucleotide sequences adjoining The method of acid sequence, methods described include：(a) by the target nucleic acid comprising known target nucleotide sequences and general oligonucleotide afterbody Joint connects；(b) part of the target nucleic acid and described general is expanded with the first adapter-primer and the first target specific primer The amplification chain of oligonucleotide tail joint；(c) produced with the second adapter-primer and the amplification of the second target specific primer by step (b) Amplicon a part；And (d) uses the first sequencing primer and the second sequencing primer to the amplification portion as caused by step (c) Divide and be sequenced.Term as used herein " target nucleic acid " is related to containing nucleotide sequence to be determined and known target nucleotide sequences The nucleic acid molecules of both.The target nucleic acid can be any length, and can be double-strand or single-stranded.Term as used herein " known target nucleotide sequences " refer to its sequence (for example, the species (identity) for the nucleotide base that the nucleic acid is included And order) known to target nucleic acid a part.Known target nucleotide sequences can be more than 10 nucleotides, preferably 30 with coker The random length (for example, 30 nucleotides, 40 nucleotides, 50 nucleotides or more nucleotides) of thuja acid.It is used herein Term refer to be located at identical nucleic acid molecule (that is, target nucleic acid) with known target nucleotide sequences " with ... adjacent nucleotide sequence " Above and it is the known upstream of target nucleotide sequences or the nucleotide sequence in downstream.It is described with ... adjacent nucleotide sequence The nucleotide sequence of random length can be included.In some embodiments, the nucleotides sequence abutted with known target nucleotide sequences Row include below 1kb nucleotide sequence, for example, below 1kb nucleotide sequence, below 750bp nucleotide sequence, Below 500bp nucleotide sequence, below 400bp nucleotide sequence, below 300bp nucleotide sequence, below 200bp The nucleotide sequence of nucleotide sequence, below 100bp.The different target nucleic acids containing known target nucleotide sequences are included in sample The situation of (for example, as it is known that target nucleotide sequences multiple cell occur in genome or on single coloured differently body) Under, multiple sequences containing " nucleotide sequence with the adjoining of known target nucleotide sequences " may be present.Term as used herein " measure nucleotide sequence " is related to the species and relative position of the nucleotide base contained by measure nucleic acid.
The methods described herein the step of in (a), general oligonucleotide pigtail connection can be connected to target nucleic acid.At some In embodiment, target nucleic acid may be included in the sample containing multiple nucleic acids, and some in the multiple nucleic acids simultaneously do not contain institute State target nucleic acid.In some embodiments, general oligonucleotide pigtail connection can be connected to substantially all of in sample Nucleic acid.In some embodiments, general oligonucleotide pigtail connection can be connected to the nucleic acid containing target nucleic acid sequence and not Both nucleic acid of nucleic acid containing target nucleic acid sequence.
Term as used herein " general oligonucleotide pigtail connection " refers to by two chains (sealed joint and amplification chain) structure Into nucleic acid molecules, the nucleic acid molecules, which include, first can connect duplex ends and the second unpaired end.General oligonucleotide The sealed joint of pigtail connection contains 5 ' double stranded sections.Amplification chain contain unpaired 5 ' part, 3 ' double stranded sections and 3 ' T it is prominent, with And with the first sequencing primer and the second sequencing primer identical nucleotide sequence.The double stranded section of sealed joint and amplification chain is substantially mutual Mend, and formed contain 3 ' T protrusions first can connect duplex ends, and the double stranded section long enough, with connection temperature Lower maintenance double chain form.
In some embodiments, comprising the amplification with the first sequencing primer and the second sequencing primer identical nucleotide sequence The part of chain can at least partly be contained in 5 ' unpaired parts of amplification chain.
In some embodiments, general oligonucleotide pigtail connection can include double stranded section and unpaired part, wherein, The unpaired part only includes 5 ' parts of amplification chain, i.e. whole sealed joint is double stranded section.
In some embodiments, general oligonucleotide pigtail connection can be Y-shaped, i.e. unpaired part can include envelope The unpaired part of closed chain and amplification both chains.The length of the unpaired part of sealed joint can be shorter than, be longer than or equal to amplification chain Unpaired part.In some embodiments, the unpaired part of sealed joint can be shorter than the unpaired part of amplification chain.Y shape General oligonucleotide pigtail connection has the advantages of unpaired part of sealed joint will not suffer from 3 ' extension in PCR schemes.
In some embodiments, the sealed joint of general oligonucleotide pigtail connection can further include 3 ' unpaired portions Point, 3 ' the unpaired part substantially not with expand chain 5 ' unpaired partial complementarities；And wherein, the 3 ' of the sealed joint Unpaired part substantially not with any Primers complementary, or is substantially different from any primer.In some embodiments, it is general The sealed joint of oligonucleotide tail joint can further include specific will not be annealed to expand chain 5 ' not at an annealing temperature The unpaired part in the 3 ' of mating section；And wherein, 3 ' unpaired parts of the sealed joint at an annealing temperature will not be special Property is annealed to any primer or its complement.
In some embodiments, the double stranded section of general oligonucleotide pigtail connection is (for example, one or both of two chains Double stranded section) length be at least seven base-pair, for example, length be more than 7bp, more than 8bp, more than 9bp, more than 10bp, More than 11bp, more than 12bp, more than 13bp or more than 14bp.In some embodiments, general oligonucleotide pigtail connection The length of double stranded section can be at least more than 30bp, for example, more than 30bp, more than 31bp, more than 32bp, more than 33bp, 34bp The above, more than 35bp, more than 40bp or more than 50bp.The double stranded section of general oligonucleotide pigtail connection should not be oversize, and The PCR amplifications of amplicon needed for (suppress) are checked in the PCR amplification schemes used.Some PCR sequencing PCRs of future generation use Y Shape linkers.These connection wye molecules need the double stranded section of finite length (for example, below 17bp), to avoid some PCR steps are (for example, library enrichment PCR (library enrichment PCR), bridge-type PCR (bridge PCR) or emulsion-based PCR (emulsion PCR)) period formation intramolecular hair fastener.Y shape general oligonucleotide pigtail connection in methods described herein is not This by the end of double-strand two is limited.This PCR checks effect and is not particularly suited for the present invention as caused by duplex ends, because two Individual target primer can be from inside close to target fragment.In some embodiments, the double stranded section of general oligonucleotide pigtail connection Length can be at least more than 18bp, for example, more than 18bp, more than 19bp, more than 20bp, more than 21bp, more than 22bp, 23bp with Upper, more than 24bp or more than 25bp.
The illustrative example of general oligonucleotide pigtail connection is shown in Fig. 9.
The connection of general oligonucleotide pigtail connection can be completed by any method as known in the art, for example, flat end End connection or TA connections.In some embodiments, before the connection of general oligonucleotide pigtail connection, can make in sample Nucleic acid experience nucleic acid end is repaired, so that the end of the nucleic acid becomes flat end.End is repaired and is well known in the present art, Related kit and/or enzyme are commercially available (for example, NEBNEXTTMEnd Repair Module (catalog number (Cat.No.) E6050L；New England Biolabs；Ipswich,MA)).
In some embodiments, before the connection of general oligonucleotide pigtail connection, the nucleic acid phosphorus in sample can be made Acidifying and/or polyadenylation.Polyadenylation can provide adenosine in 3 ' ends of nucleic acid and protrude (adenosine overhang).So Afterwards, the first nucleic acid can be connected to by the second nucleic acid that TA connections there will be thionine (thionine) 3 ' prominent.Connection method exists Known in the art, related kit and/or enzyme are commercially available, for example, can be by NEBNEXTTM da-Tailing Module (catalog number (Cat.No.) E6053L:New England Biolabs；Ipswich, MA) it is used to make the flat terminal adenosine acidifying of nucleic acid. In some embodiments, it is possible to provide there is the prominent general oligonucleotide pigtail connection of thionine 3 '.
The step of methods described herein (b) and step (c) can each include PCR amplification schemes, i.e. polymerase chain reaction Answer (PCR) amplification cycles group.Term as used herein " amplification scheme " refers to specific amplification nucleotide sequence interested The program of (that is, the abundance for increasing nucleotide sequence interested), more specifically, when previous polymerase extension products are as successive More wheels extension template when, exponential amplification occur.At least one, preferably at least 5 are included according to the PCR of present invention amplification schemes Repetitive cycling more than individual, wherein, each circulation comprises the following steps：1) chain separation (for example, thermal denaturation)；2) antisense oligonucleotide primer Thing is annealed to template molecule；And 3) the nucleic acid polymerase extension of annealing primer.These steps each required condition and time It can be formulated by those of ordinary skill in the art.Carried out according to the amplification scheme of methods described herein preferably in thermal cycler, Many thermal cyclers are commercially available.
PCR needs to use nucleic acid polymerase.Phrase " nucleic acid polymerase " used herein refers to be catalyzed ribonucleoside triphosphote Template-dependent polymerization, to form the enzyme of the primer extension product complementary with template nucleic acid sequence.Nucleic acid polymerase is being annealed 3 ' the ends starting synthesis of primer, and carried out towards the direction of the end of template 5 '.Many nucleic acid polymerases are in the art Know and commercially available.One group of preferable nucleic acid polymerase is heat-staple, i.e. they are enough to make moving back for complementary nucleic acid experienced After the temperature (for example, 94 DEG C) or sometimes higher temperature of the denaturation of fiery chain, still reservation function.
As understood in the art, PCR needs the circulation for including chain separation step, and the chain separation step, which is usually directed to, to be added Thermal reaction mixture.Term as used herein " chain separation " refers to handle nucleic acid samples " by chain separation ", to cause complementation Duplex molecule be separated into can be annealed to two of Oligonucleolide primers it is single-stranded.More specifically, according to the chain of methods described herein Separation by nucleic acid samples by being heated above its TmAnd realize.Typically in the buffer solution suitable for nucleic acid polymerase For sample containing nucleic acid molecules, it is heated to 94 DEG C and is enough to realize chain separation.Exemplary buffer solution contains 50mM KCl, 10mM Tris-HCl(pH 8.8@25℃)、0.5-3mM MgCl2And 0.1%BSA.
Also as understood in the art, PCR is needed primer annealing to template nucleic acid.Any chain of target nucleic acid all can be mould Plate nucleic acid, because template nucleic acid is defined as the given specific single-chain nucleic acid that be annealed to thereon of primer meeting.It is used herein " annealing " refers to the nucleic acid strand for allowing two complementary nucleic acid chains or being substantially complementary, more specifically, when the situation in PCR Down in use, referring to the nucleic acid strand for allowing two complementary nucleic acid chains or being substantially complementary, Template Dependent is formed to cause The primer extend substrate of polymerase.The condition of primer-target nucleic acid annealing changes with primer length and sequence, and is based on being calculated Primer Tm.Generally, the annealing steps in amplification scheme, which are included in after chain separation step, is reduced to temperature based on being calculated Primer sequence TmThe temperature sufficiently long time, to allow thus to anneal.TmCan be by those skilled in the art using largely applying extensively Any of algorithm is easily predicted (for example, obtainable OLIGO on internetTM(Molecular Biology Insights Inc.Colorado) primer-design software and VENTRO NTITM(Invitrogen, Inc.California) draws Thing design software and program, including Primer3, Oligo Calculator and NetPrimer (Premier Biosoft；Palo Alto, CA；And in WWW http://www.premierbiosoft.com/netprimer/netprlaunch/Help/ Provided free on xnetprlaunch.ht ml)).For example, the T of primermCalculated using below equation, the formula is NetPrimer softwares use and in Frieir etc. PNAS 1,986 83:More detailed description in 9373-9377 be present, with The mode of reference is integrally incorporated herein.
Tm=Δ H/ (Δ S+R*ln (C/4))+16.6log ([K+]/(1+0.7[K+]))-273.15
Wherein, Δ H is the enthalpy of spiralization；Δ S is the entropy of spiralization；R is mol gas constant (1.987cal/ DEG C of * mol)；C is nucleic acid concentration；And [K+] it is salinity.For most of amplification schemes, annealing temperature is selected below pre- Survey TmAbout 5 DEG C, although can be used closer to TmWith higher than TmTemperature (for example, less than prediction TmTemperature between 1 DEG C and 5 DEG C Or higher than prediction TmTemperature between 1 DEG C and 5 DEG C), for example, less than prediction TmMore than 5 DEG C temperature (e.g., low 6 DEG C, it is low 8 DEG C, Low 10 DEG C or lower) equally can be with.Generally, annealing temperature is closer to Tm, anneal more special.Allow during PCR amplification schemes The time of primer annealing depends greatly on the volume (larger volume needs the longer time) of reaction, while also takes Certainly (relative concentration of relatively low primer and template is compared, higher relative concentration needs less in the concentration of primer and template Time).According to volume and relative primer/template concentrations, the primer annealing step in amplification scheme may be about -5 minutes 1 second, But would generally be between 10 seconds and 2 minutes, preferably about -2 minutes 30 seconds." substantially annealing " used herein refers to It is enough the annealing grade of specific amplification products for producing detectable level in PCR amplification schemes.
PCR also relies on the polymerase extension of annealing primer in each cycle." polymerase prolongs term as used herein Stretch " refer to 3 ' ends that at least one complementary nucleotide is added to annealing primer by nucleic acid polymerase in a manner of Template Dependent On.The preferred addition more than one nucleotides of polymerase extension, preferably add up to and including the nucleotides corresponding to template total length. The condition of polymerase extension changes with polymerase species.Temperature for polymerase extension is typically based on the known activity of enzyme Matter.Although in the case where annealing temperature needs for the such as less than most ideal temperature of enzyme, using relatively low elongating temperature often It is and acceptable.Generally, although enzyme remains with least partly activity when less than its most preferable elongating temperature, by the most frequently used The polymerase that heat-stabilised poly synthase (for example, Taq polymerase and its variant) is carried out extends in 65 DEG C -75 DEG C, preferably from about 68 DEG C -72 DEG C carry out.
Primer extend is carried out under conditions of the Oligonucleolide primers extension of annealing is allowed.Term as used herein " permits Perhaps the oligonucleotides annealed extends to cause condition that extension products generate " refer to including such as temperature, salinity and it is auxiliary because The nucleic acid polymerases such as sub- concentration, pH and enzyme concentration are catalyzed the set of the condition of primer extend under such conditions.These conditions will Change with the species of nucleic acid polymerase used, but the condition of many useful polymerases is well-known to those skilled in the art. One exemplary collection of condition is 50mM KCl, 10mM Tris-HCl (25 DEG C of 8.8@of pH), 0.5-3mM MgCl2、dNTP Each 200 μM and 0.1%BSA, 72 DEG C, Taq polymerase is catalyzed primer extend under these conditions.The condition of starting and extension is usual Being included in suitable buffer solution, (" buffer solution " includes solvent (being usually water-based) in the case, plus necessary co-factor And influence pH, the reagent of ionic strength etc.) in and at a suitable temperature, at least one be present but be more preferably the presence of all Four kinds of different deoxyribonucleoside triphosphates and polymerisation induced agent (such as archaeal dna polymerase or reverse transcriptase).
In some embodiments, each amplification step may include that length expands scheme for the PCR of -20 circulations of 5 circulations Circulation group.In some embodiments, each amplification step may include that length expands scheme for the PCR of -20 circulations of 10 circulations Circulation group.In some embodiments, each amplification step may include that length expands scheme for the PCR of -16 circulations of 12 circulations Circulation group.In some embodiments, annealing temperature can be less than 70 DEG C.In some embodiments, annealing temperature can be with low In 72 DEG C.
In different embodiments, method described herein and composition are related to this paper institutes with one or more types State primer and enter performing PCR amplification scheme." primer " used herein is to refer to specificity to be annealed to polynucleotide template and carry 3 ' ends of the substrate of template dependent polymerase are provided as, to produce the extension products complementary with the polynucleotide template DNA or RNA polynucleotide molecules or its analog.Useful primer is typically single-stranded in methods described herein, and primer And its complement can anneal to form double-stranded polynucleotide.It is smaller than according to the length of methods described herein and the primer of composition Or equal to 300 nucleotides, for example, length be less than or equal to 300 or 250 or 200 or 150 or 100 or 90 or 80 or The nucleotides of 70 or 60 or 50 or 40 or 30 or less or 20 or less or 15 or less but at least 10 Nucleotides.The method for preparing primer be it is known in the art that and many commercial sources provide be adapted to provide for according to described herein The oligonucleotide synthesis service of the primer of method and composition, for example, INVITROGENTMCustom DNA Oligos；Life Technologies；Grand Island, NY or the custom DNA Oligos from IDT；Coralville, IA.
In some embodiments, in the nucleic acid being connected to general oligonucleotide pigtail connection in sample (for example, target nucleus Acid) after, the target nucleic acid can be expanded in the first amplification step (i.e. step (b)).First amplification step can be to use The PCR amplification cycles groups that first target specific primer and the first pigtail connection primer are carried out.
Term as used herein " the first target specific primer " refers to containing specificity being annealed at an annealing temperature The single stranded oligonucleotide of the nucleotide sequence of target nucleic acid.
In some embodiments, the first target specificity primer can include 5 ' sequence label parts.In some embodiment party In formula, all first target specific primers present in reaction can include the sequence label of identical 5 ' part.In multi-PRC reaction In, different primers species can be interacted with each other by the undesirable mode of missing the target, and be drawn so as to cause by what archaeal dna polymerase was carried out Thing extends and subsequent amplification.These primer dimers are usually short, and their efficient amplification leading reaction and can occupy excellent Gesture, so as to cause the amplification of required target sequence bad.Include in the first target specific primer 5 ' sequence labels cause it is any Potential primer dimer (it can cause to contain identical complementation afterbody two ends).In subsequent PCR cycle, primer Dimer will be denatured into single-stranded DNA primer dimer, and each single-stranded DNA primer dimer contains on two end by 5 ' marks Sign the complementary series introduced.Be not primer annealing to these single-stranded DNA primer dimers, but preferentially occur intramolecular hair fastener The formation of (panhandle shape structure), this is due to the close accessibility of complementary label on same primers dimer molecule (proximate accessibility), rather than the intermolecular interaction on different molecular with new primer.Result is these Primer dimer is very difficult to expand, so that primer will not be consumed exponentially by the amplification of undesirable dimer.Phase Instead, for the specific amplification of desired target sequence, the primer of tape label can keep high and enough concentration.Primer dimerization The accumulation of body can also damage multiplex PCR, because primer dimer competes and consumes other reagents in reaction.In some embodiment party In formula, 5 ' sequence labels can be the sequence rich in GC, i.e. sequence label contains at least 50% G/C content, at least 55% G/C content, at least 60% G/C content, at least 65% G/C content, at least 70% G/C content, at least 75% G/C content, extremely Few 80% G/C content or higher G/C content.In some embodiments, sequence label contains containing at least 60% GC Amount.In some embodiments, sequence label contains at least 65% G/C content.
Term as used herein " the second target specific primer " refers to containing 3 ' partly single strand oligonucleotides with 5 ' parts Acid, described 3 ' partly containing can specificity be annealed to the known target nucleotide sequences that the amplicon as caused by step (b) includes A part nucleotide sequence, described 5 ' partly contain and the second sequencing primer identical nucleotide sequence.Second target-specific draws Thing is nested relative to the first target specific primer.In some embodiments, the second target specific primer passes through at least three nucleosides Acid (for example, by more than 3, more than 4, more than 5, more than 6, more than 7, more than 8, more than 9, more than 10, Or more than 15 nucleotides) nested relative to the first target specific primer.
In some embodiments, all second target specific primers being present in reaction contain the part of identical 5 '. In some embodiments, 5 ' partly can be used to check described by the 5 ' labels described above on the first target specific primer Primer dimer.
In some embodiments, the first target specific primer and the second target specific primer are substantially same with target nucleic acid One chain complementation.In some embodiments, specificity is annealed to the first target specific primer and the second target of known target sequence The part of specific primer can include exclusive (unique) base of at least 20 known target nucleotide sequences altogether, example Such as, more than 20 exclusive bases, more than 25 exclusive bases, more than 30 exclusive bases, more than 35 exclusive bases, 40 with Upper exclusive base or more than 50 exclusive bases.In some embodiments, specificity is annealed to the first target of known target sequence The part of specific primer and the second target specific primer is only containing at least 30 altogether known target nucleotide sequences There is base.
Term as used herein " the first adapter-primer " refers to containing 5 ' the part identical cores with the first sequencing primer The nucleic acid molecules of acid sequence.Because the first pigtail connection primer is thus identical (with complementation with least a portion of amplification chain-ordering Relatively), the first pigtail connection primer will not be able to specificity and be annealed to general oligonucleotide pigtail connection any in itself Part.
Term as used herein " the second adapter-primer " refers to containing a part of identical core with the first sequencing primer Acid sequence and relative to the nested nucleic acid molecules of the first adapter-primer.Because the second pigtail connection primer is thus with expanding chain sequence At least a portion of row is identical (relative with complementation), and the second pigtail connection primer will not be able to specificity and be annealed to general widow Any part of nucleotides pigtail connection in itself.In some embodiments, the second adapter-primer is identical with the first sequencing primer.
Second adapter-primer should be nested relative to the first adapter-primer, i.e. first adapter-primer include with Chain identical nucleotide sequence is expanded, the sequence is simultaneously not included in second adapter-primer and drawn with being contained in the second joint The position for being Comparatively speaking located at the 5 ' ends for being closer to amplimer with amplification any sequence of chain identical in thing.In some realities Apply in mode, the second adapter-primer by least three nucleotides (for example, by 3 nucleotides, by 4 nucleotides, pass through 5 Individual nucleotides, by 6 nucleotides, by 7 nucleotides, by 8 nucleotides, by 9 nucleotides, pass through 10 nucleosides Acid or more nucleotides) it is next nested.
In some embodiments, the first adapter-primer contains with the amplification chain of general oligonucleotide pigtail connection most About 20 base identical nucleotide sequences at 5 ' ends, and the second adapter-primer can include the expansion with general oligonucleotide pigtail connection About 30 base identical nucleotide sequences of chain, 5 ' bases of second adapter-primer are on 3 ' directions away from the amplification chain 5 ' end at least three nucleotides (terminus of the of 3 ' of the of at least 3nucleotides 5 ' amplification strand)。
The use of nested adaptor primer, which eliminates, to be generated amplifiable (for example, in bridge-type PCR or emulsion-based PCR) but can not be sequenced Final amplicon possibility, this is situation about possible occurring in half-nest type (hemi-nested) method.In other situations Under, using the half-nest type method carried out with sequencing primer identical primer undesirable amplified production can be caused to be walked from the first PCR Suddenly leave to the 2nd PCR steps, and will finally produce artificial sequencing read.As described herein, the use of two adapter-primers can To reduce these problems, and these problems can be eliminated in some embodiments.
In the first PCR amplification cycles of the first amplification step, the first target specific primer can specificity be annealed to containing The template strand of any nucleic acid of known target nucleotide sequences.According to the direction of the first target specific primer of design, by known to synthesis Target nucleotide sequences upstream or downstream and the sequence complementary with template strand.If during the PCR extension stage, the 5 ' of template strand End terminates at the general oligonucleotide pigtail connection of connection, and 3 ' ends of the product chain newly synthesized will be contained and the first afterbody The complementary sequence of adapter-primer.In subsequent PCR amplification cycles, the first target specific primer and the first pigtail connection primer two Person specific will can be annealed to the appropriate chain of target nucleic acid sequence, it is known that target nucleotide sequences and general oligonucleotide pigtail connection Between sequence can be amplified (that is, replicate).
In the next step (that is, step (c)) of methods described herein, amplification is by step (b) in the second amplification step A part for caused amplification part.Second amplification step can be to be carried out using the second target specific primer and the first sequencing primer PCR amplification cycles groups.2nd PCR amplification cycles group can have identical or not with the PCR parameters in the first PCR amplification cycles groups Same PCR parameters.For example, the PCR amplifications scheme of step (b) and step (c) can have identical or different annealing temperature or Identical or different extension step duration.
Method described herein allow measure one of both sides of known target nucleotide sequences or both sides with it is described known The nucleotide sequence of target nucleotide sequences adjoining.No matter target nucleic acid is normally in the form of single-chain nucleic acid or double-strandednucleic acid Form is present, and sequence information is generally represented with single-stranded form (chain A) from 5 ' to 3 '.If chain A known target nucleus glycosides will be determined The sequence at 5 ' ends of acid sequence, gene-specific primer can be complementary (that is, being annealed to chain A) with chain A.If it will determine chain A's The sequence at 3 ' ends of known target nucleotide sequences, gene-specific primer can be identical with chain A, to cause the primer to be annealed to The complementary strand of double chain target acid.Such design of primers is thought of as well known to those of ordinary skill in the art.
In some embodiments, it is as described herein to be directed to use with the first gene-specific primer and the second gene specific The method of primer may be such that analysis has outstanding target-hit (on-target) rate, such as 70-90%.In some embodiments In, analysis as described herein and method can be with least 85% special rates of target.
In some embodiments, by four class design of primers be primer under about 61-72 DEG C of annealing temperature (for example, about 61-69 DEG C, about 63-69 DEG C, about 63-67 DEG C, about 64-66 DEG C) by specificity be annealed to their complementary series.In some implementations It is that specificity is annealed to their complementary sequence by primer under the annealing temperature less than 72 DEG C by four class design of primers in mode Row.In some embodiments, it is that specificity is annealed to by primer under the annealing temperature less than 70 DEG C by four class design of primers Their complementary series.In some embodiments, it is that primer will under the annealing temperature less than 68 DEG C by four class design of primers Specificity is annealed to their complementary series.In some embodiments, it is that primer moves back at about 65 DEG C by four class design of primers Specificity is annealed to their complementary series at fiery temperature.
In some embodiments, specificity be annealed to the part of the target specific primer of known target nucleotide sequences will be (for example, about 61-69 DEG C, about 63-69 DEG C, about 63-67 DEG C, about 64-66 DEG C) specificity annealing at a temperature of about 61-72 DEG C. In some embodiments, the part that specificity is annealed to the target specific primer of known target nucleotide sequences will be in PCR buffer solutions In at a temperature of about 65 DEG C specificity annealing.
In some embodiments, primer and/or joint as described herein can not contain the base of modification (for example, primer And/or joint can not contain 3 ' amine of closing (amine of blocking 3 ')).
In the next step (that is, step (d)) of methods described herein, the amplification part caused by step (c) can be entered Row sequencing.In some embodiments, sequencing can be carried out by PCR sequencing PCR of future generation." next generation's sequencing " used herein is Refer to such oligonucleotide sequencing technology：The oligonucleotide sequencing technology have with higher than traditional sequencing methods (for example, Sanger Sequencing) possible speed speed ability that oligonucleotides is sequenced because the sequencing parallel execution of future generation and reading The even millions of individual sequencing reactions of access thousand.The non-limiting examples of PCR sequencing PCR/platform of future generation include：Extensive parallel signature It is sequenced (Lynx Therapeutics)；454 pyrosequencings (454Life Sciences/Roche Diagnostics)；Gu (Solexa/Illumina) is sequenced in mutually reversible Dye Terminator thing：SOLiD technologies (Applied Biosystems)；Ion semiconductors It is sequenced (ION Torrent)；(Complete Genomics) is sequenced in DNA nanospheres；And can be from Pacific Biosciences, Intelligen Bio-systems, Oxford Nanopore Technologies and Helicos The technology that Biosciences is obtained.In some embodiments, sequencing primer can include can be simultaneous with selected PCR sequencing PCR of future generation The part of appearance.The limitation of sequencing technologies and relevant primer of future generation and design parameter be well known in the present art (see, for example, Shendure etc., " Next-generation DNA sequencing ", Nature, 2008, volume 26, the 10th phase, 1135- 1145；Mardis, " The impact of next-generation sequencing technology on Genetics ", Trends in Genetics, volume 2007,24, the 3rd phase, the 133-141 pages；Su etc., " Next- Generation sequencing and its applications in molecular diagnostics ", Expert Rev Mol Diagn, 2011,11 (3):333-43；Zhang etc., " The impact of next-generation Sequencing on genomics ", J Genet Genomics, 2011,38 (3):95-109；Nyren, P. etc., Anal Biochem 208:17175(1993)；Bentley, D.R., Curr Opin Genet Dev16:545-52(2006)； Strausberg, R.L. etc., Drug Disc Today 13:569-77(2008)；U.S. Patent number 7,282,337；The U.S. is special Profit number 7,279,563；U.S. Patent number 7,226,720；U.S. Patent number 7,220,549；U.S. Patent number 7,169,560；It is beautiful State's patent No. 6,818,395；U.S. Patent number 6,911,345；US publication 2006/0252077,2007/0070349 and 20070070349, be integrally incorporated by reference herein).
In some embodiments, sequencing steps depend on the use of the first sequencing primer and the second sequencing primer.One It is compatible PCR sequencing PCR of future generation as described herein by the first sequencing primer and the selection of the second sequencing primer in a little embodiments.
It is this area that read, which will be sequenced, with the method that the known array database of genome and/or cDNA sequence is compared In it is known, and be commercially available for the software of this process.In some embodiments, Complete Mappings (map) are not extremely The read (removing sequencing primer and/or joint nucleotide sequence) of wild-type sequence database can be genome rearrangement or large-scale slotting Enter missing (indel) mutation.In some embodiments, (gone containing the read for mapping to the sequence of multiple positions in genome Fall sequencing primer and/or joint nucleotide sequence) can be genome rearrangement.
In some embodiments, can before or after step a- steps d arbitrary steps, by target nucleic acid and/or Its amplified production separates from enzyme, primer or buffer composition.Method for seperated nuclear acid is well known in the art. In some embodiments, separation may include the reversible fixation of solid phase (Solid Phase Reversible Immobilization, SPRI) purify.SPRI purification process is known in the art, and kit is commercially available, for example, Agencourt AMPure XP-PCR purify (catalog number (Cat.No.) A63880, Beckman Coulter；Brea, CA).In some embodiments, enzyme can Inactivated by heating.
In some embodiments, target nucleic acid may be included in genomic DNA.In some embodiments, target nucleic acid can It is contained in ribonucleic acid (RNA), for example, mRNA.In some embodiments, target nucleic acid may be included in cDNA.It is many suitable Optimal read length is provided in the sequence measurement for methods described herein to run for the sequencing of tens of to hundreds of nucleotide bases (for example, Ion Torrent technologies can produce 200-400bp read length).For example, included by genomic DNA or mRNA Target nucleic acid may be included in and be significantly longer than in the nucleic acid molecules of this optimal read length.In order that expand caused by step (c) Increasing nucleic acid moiety turns into the length that may be adapted in specific sequencing technologies use, it is known that target nucleotide sequences and target nucleic acid end Average distance between (general oligonucleotide pigtail connection can be connected to the end) should be as close possible to selected technology Optimal read length.For example, if the optimal read length of given sequencing technologies is 200bp, expanded according to methods described herein The nucleic acid molecules of increasing should have about below 400bp average length.Before step (a), can to by such as genomic DNA or The target nucleic acid that mRNA is included is sheared (for example, mechanical shearing or enzymatic shearing), to produce the fragment of any required size. The non-limiting examples of mechanical shearing method include：Ultrasound, atomization and the AFA that can be obtained from Covaris (Woburn, MA)TM Shearing technique.In some embodiments, mechanical shearing can be carried out by the target nucleic acid that ultrasound is included to genomic DNA. In some embodiments, when target nucleic acid is included by RNA, reverse transcriptase scheme can be subjected the sample to generate DNA profiling, so After the DNA profiling can be sheared.In some embodiments, target RNA can be carried out before reverse transcriptase scheme is carried out Shearing.In some embodiments, the sample containing target RNA can be used for following method as described herein：Using from fresh sample Or the total nucleic acid of degraded sample extraction；Genomic DNA need not be removed for cDNA sequencings；Without making ribosomes for cDNA sequencings RNA exhausts；Mechanical shearing or enzymatic shearing are not needed in any step；Make RNA experience double by using random hexamer Chain cDNA is synthesized；And by making nucleic acid undergo end reparation, phosphorylation and polyadenylation in single pipe.
In embodiments, it is known that target nucleotide sequences may be included in gene rearrangement.Method described herein is fitted Presence and/or species together in measure gene rearrangement, because only the species of the gene rearrangement of half must be previously known (that is, treating the half gene rearrangement targetted by gene-specific primer).In some embodiments, gene rearrangement can include cancer Gene.In some embodiments, gene rearrangement can include fusion oncogene.
In some embodiments, target nucleic acid may be included in sample.In some embodiments, target nucleic acid may be included in It is derived from the sample of subject.In some embodiments, sample can be the diagnosis sample for being derived from subject.In some realities Apply in mode, sample can further include protein, cell, fluid, biofluid, protective agent, and/or other materials.With non- The mode of limitative examples, sample can be cheek swab (cheek swab), blood, serum, blood plasma, phlegm, cerebrospinal fluid, urine Liquid, tear, alveolar isolate (alveolar isolates), liquor pleurae, pericardial fluid, cyst fluid (cyst fluid), tumor group Knit, organize, slicer, saliva, extract (aspirate), or the combination of above-mentioned substance.In some embodiments, sample Product can be obtained by resection or slicer.
In some embodiments, sample is available from needing the subject for the treatment of cancer.In some embodiments, sample Product can include tumor cell group, for example, the group of at least one tumour cell.In some embodiments, sample can include tumour Biopsy's piece, including but not limited to untreated biopsy or treated biopsy are (for example, formalin is fixed Biopsy and/or FFPE biopsy).
In some embodiments, sample fresh can be collected.In some embodiments, sample can be used for this paper institutes Before in the method and composition stated, the sample is stored.In some embodiments, sample is undressed sample. " undressed sample " used herein refers in addition to being diluted in solution and/or being suspended in solution, not carry out The biological sample of any prior sample pretreatment.In some embodiments, sample is available from subject, and can for It is preserved or processed before method described herein and composition.By way of non-limiting example, can be by sample bag It is embedded in paraffin, refrigerate or freezes.It is able to will be freezed before the presence according to method described herein and composition measuring nucleic acid Sample thaw.In some embodiments, sample can be finished or treated sample.For processing or processed sample Illustrative methods include but is not limited to：Centrifugation, filtering, ultrasound, homogenize, heat, freeze and thaw, with protective agent (for example, Anticoagulant or nucleic acid inhibitor) contact, and any combination of the above method.In some embodiments, chemistry can be used Reagent and/or biological reagent are handled sample.Chemical reagent and/or biological reagent can be used in processing and/or storage period Between protection and/or keep the stability of contained nucleic acid in sample or sample.Alternatively or additionally, chemical reagent can be used And/or biological reagent makes nucleic acid be discharged from other components of sample.By way of non-limiting example, for this paper institutes Before the method and composition stated, blood sample can be handled with anticoagulant.Those skilled in the art are known to be used for foranalysis of nucleic acids Sample processing, preserve or processing method and process.In some embodiments, sample can be obtained for example by centrifugation Clear fluid sample.In some embodiments, by low-speed centrifugal (for example, 3000 × below g) and can collect containing clarification The supernatant of fluid sample clarifies sample.
In some embodiments, can be before for method described herein and composition, to core present in sample Acid is separated, is enriched with or purified.The method of separation, enrichment or purification of nucleic acid is those of ordinary skill in the art institute from sample It is known.By way of non-limiting example, the kit for the isolated genes group DNA from various sample types is commercially available (for example, catalog number (Cat.No.) 51104,51304,56504 and 56404；Qiagen；Germantown, MD).
Method described herein can be used for multiple (multiplex) technology.It is more in the embodiment of methods described herein Application can include measure and the nucleotide sequence of target nucleotide sequences adjoining known to one or more again.It is used herein " multiplex PCR " refers to the PCR modifications expanded while carrying out more than one target nucleic acid in a reaction vessel and then passed through The sequence of amplified production is measured using more than one group of first gene-specific primer and the second gene-specific primer.It is more It can relate to detect the different target sequence of about 2-1,000 kinds in single reaction again.It is used herein multiple to refer to single anti- Should in detection 2-1, the different target sequences of any scope (for example, between 5-500,25-1000 or 10-100 kind) between 000 kind Row etc..Mean to exist reacting same PCR suitable for PCR term " multiple " has at least two different target sequences Specific primer.
In some embodiments, can be with multiple first target specific primers and the second target specific primer to sample or sample Target nucleic acid in the unitary part of product is expanded.In some embodiments, the multiple first target specific primer and Two target specific primers may be present in single reactant mixture, for example, a variety of amplifications can be produced in same reactant mixture Product.In some embodiments, multigroup first target specific primer and the second target specific primer can specificity be annealed to not Known target sequence included in homogenic.In some embodiments, at least two group of first target specific primer and the second target Specific primer specific can be annealed to the different piece of known target sequence.In some embodiments, at least two group of first target Specific primer and the second target specific primer specific can be annealed to the different portions for the known target sequence that individual gene is included Point.In some embodiments, at least two group of first target specific primer and the second target specific primer can specificity be annealed to The different extrons of gene containing known target sequence.In some embodiments, multiple first target specific primers can contain The sequence label of identical 5 ' part.
In the embodiment of methods described herein, multiple application may include to survey in a sequencing reaction or sequencing operation In fixed multiple samples with one or more known to target nucleotide sequences adjoining nucleotide sequence.Multiple samples can be different next Source, for example, coming from different tissues and/or different subjects.In such embodiment, general oligonucleotide pigtail connection can enter One step includes bar code part.In some embodiments, can be by the general oligonucleotide afterbody with unique bar code part Joint is added in each sample, and is connected with nucleic acid therein；Then the sample can be merged after step (a).Amplification Thus each sequencing read obtained by product will all include the bar code of sample type of the identification containing primary template nucleic acid, described Amplified production is derived from the primary template nucleic acid.The use of bar code part is known in the art in next generation's sequencing application , and be described in following works：For example, Margulies, M. etc., " Genome Sequencing in Microfabricated High-Density Picolitre Reactors ", Nature, 437,376-80 (2005)； Mikkelsen, T. etc., " Genome-Wide Maps of Chromatin State in Pluripotent and Lineage-Committed Cells ", Nature, 448,553-60 (2007)；McLaughlin, S. etc., " Whole- Genome Resequencing With Short Reads:Accurate Mutation Discovery With Mate Pairs and Quality Values ", ASHG Annual Meeting (2007)；Shendure I. etc., " Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome ", Science, 309,1728- 32(2005)；Harris, T. etc., " Single-Molecule DNA Sequencing of a Viral Genome ", Science, 320,106-9 (2008)；Simen, B. etc., " Prevalence of LoW Abundance Drug Resistant Variants by Ultra Deep Sequencing in Chronically HIV-infected Antiretroviral (ARV) Naive Patients and the Impact on Virologic Outcomes ", 16th International HIV Drug Resistance Workshop, Barbados (2007)；Thomas, R. etc., “Sensitive Mutation Detection in Heterogeneous Cancer Specimens by Massively Parallel Picoliter Reactor Sequencing ", Nature Med., 12,852-855 (2006)；Mitsuya,Y Deng " Minority Human Immunodeficiency Virus Type 1Variants in Antiretroviral- Naive Persons With Reverse Transcriptase Codon 215Revertant Mutations ", I.Vir., 82,10747-10755 (2008)；Binladen, J. etc., " The Use of Coded PCR Primers Enables High-Throughput Sequencing of Multiple HomologAmplification Products By 454Parallel Sequencing ", PLoS ONE, 2, e197 (2007)；And Hoffmann, C. etc., " DNA Bar Coding and PyROS1equencing to Identify Rare HIV Drug Resistance Mutations ", Nuc.Acids Res., 35, e91 (2007), are fully incorporated herein by reference.
In some embodiments of technology described herein, determining can carry with the sequence of known oligonucleotides target sequence adjoining For the information related to treatment disease, and/or may be included in the method for the treatment of disease.In some embodiments, sample can From the subject for needing the treatment disease related to hereditary change.In embodiments, it is known that oligonucleotides target sequence It may be included in disease related gene (for example, oncogene).In some embodiments, abutted with known oligonucleotides target sequence Sequence and/or the known oligonucleotides target sequence containing the related mutation of disease or genetic abnormality, for example, SNP, inserting Enter, delete and/or gene rearrangement.In some embodiments, it is present in being abutted with known oligonucleotides target sequence in sample Sequence and/or the known oligonucleotides target sequence may be included in gene rearrangement product.In some embodiments, gene Rearrangement can be oncogene, for example, fusion oncogene.
Some treatments of cancer are especially effective for the tumour containing specific oncogene, for example, the given fusion cancer base of targeting The therapeutic agent of effect or the expression of cause can be effective for the tumour containing the fusion oncogene, but for lacking the fusion oncogene Tumour it is invalid.Method described herein can allow the spy to disclosing oncogene state (for example, mutation, SNP and/or rearrangement) Sequencing row are measured.As described herein, when known to the only sequence of side, method described herein can further allow Particular sequence is determined, for example, in the case of unknown in exact position before carrying out methods described herein and/or rearrangement companion, Method described herein can determine presence and the species of the gene rearrangement for being related to known oncogene.
In some embodiments, the techniques described herein are related to the method for the treatment of cancer, and methods described includes：According to this Method described in text, detection are derived from what one or more oncogenes in the tumor sample for the subject for needing treating cancer were reset In the presence of；Give the effective treatment of cancer of tumour for being reset with any oncogene detected.In some embodiments, Whether the techniques described herein are related to measure needs the subject for the treatment of cancer can be described to giving the method that respond for the treatment of Method includes：According to method described herein, detection is derived from the presence that oncogene is reset in the tumor sample of subject；Its In, if detecting the presence of oncogene rearrangement, the subject is confirmed as making the treatment for targetting oncogene rearrangement product Go out response.
In some embodiments, for example, when sample is derived from and needs to treat the subject of lung cancer, it is known that oligonucleotides Target sequence can include the sequence of the gene in being selected from the group：ALK, ROS1 and RET.It is related to ALK, ROS1 and RET gene simultaneously The gene rearrangement for causing to merge oncogene is well known in the present art (see, e.g., Soda etc., Nature 2007448561-6；Rikova etc., Cell 2007131:1190-1203；Kohno etc., Nature Medicine 201218: 375-7；Takouchi etc., Nature Medicine 201218:378-81；It is integrally incorporated by reference herein). However, the exact position (for example, the position of generation is reset in ALK, ROS1 and/or RET gene) of gene rearrangement and be related to weight The species of the second gene of row can change.In method described herein, the position of rearrangement can needed not know about or be related to In the case of the species of second gene of gene rearrangement, presence and species to such rearrangement detect.
In embodiments, it is known that target sequence can include the sequence of the gene in being selected from the group：ALK、ROS1 And RET.In some embodiments, at least one set of first target specific primer and the second target specific primer can be selected from by with The group that lower primer is formed：SEQ ID NO：5 and SEQ ID NO：6；SEQ ID NO：7 and SEQ ID NO：8；SEQ ID NO： 9 and SEQ ID NO：10；SEQ ID NO：11 and SEQ ID NO：12；SEQ ID NO：13 and SEQ ID NO：14；SEQ ID NO：15 and SEQ ID NO：16；SEQ ID NO：17 and SEQ ID NO：18；SEQ ID NO：19 and SEQ ID NO：20；SEQ ID NO：21 and SEQ ID NO：22；SEQ ID NO：23 and SEQ ID NO：24；SEQ ID NO：25 and SEQ ID NO：26； SEQ ID NO：27 and SEQ ID NO：28；SEQ ID NO：29 and SEQ ID NO：30；SEQ ID NO：31 and SEQ ID NO：32；SEQ ID NO：33 and SEQ ID NO：34；SEQ ID NO：35 and SEQ ID NO：36；And SEQ ID NO：37 With SEQ ID NO：38.
In some embodiments, the presence for being derived from ALK gene rearrangement in the sample of the tumour of subject can be explained, The tumour is easily influenceed by the treatment carried out with the therapeutic agent in the group by following material composition：ALK inhibitor, gram Azoles for Buddhist nun (PF-02341066), AP26113, LDK378,3-39, AF802, IPI-504, ASP3026, AP-26113, X-396, GSK-1838705A, CH5424802, the diaminourea inhibitor of ALK kinase activity and aminopyrimidine inhibitor are (for example, NVP- TAE684 and PF-02341066) (see, e.g., Galkin etc., Proc Natl Acad Sci USA, 2007,104:270- 275；Zou etc., Cancer Res, 2007,67:4408-4417；Hallberg and Palmer F1000Med Reports 20113:21；And Sakamoto etc., Cancer Cell 201119:679-690)；And disclosed in WO 04/079326 Molecule.Above-mentioned all bibliography are integrally incorporated herein by reference.ALK inhibitor may include to reduce ALK or its portion The expression divided and/or any reagent of kinase activity, including for example, reduce ALK or part thereof expression and/or the few core of activity Thuja acid, small molecule and/or peptide." anaplastic lymphoma kinase " or " ALK " used herein refer to lead in wild-type form Often it is related to the transmembrane tyrosine kinase of neuron regulation.The ALK gene of many species and mRNA nucleotide sequence be it is known, Including people (such as SEQ ID NO：2 (mRNA), NCBI Gene ID：238).
In some embodiments, being derived from the presence of ROS1 gene rearrangement in the sample of the tumour of subject can say Bright, the tumour is easily influenceed by the treatment carried out with the therapeutic agent in the group by following material composition：ROS1 suppresses Agent and ALK inhibitor as described above (for example, gram azoles replaces Buddhist nun).ROS1 inhibitor may include the expression for reducing ROS1 or part thereof And/or any reagent of kinase activity, including for example, reduce ROS1 or part thereof expression and/or the oligonucleotides of activity, small Molecule and/or peptide.It is used herein " c-ROS1 oncogenes 1 " or " ROS1 " (being also referred to as ROS1-1 in the art) refer to The transmembrane tyrosine kinase of the sevenless subfamilies of PTPN6 interactions.The ROS1 genes of many species and mRNA nucleosides Acid sequence is known, including people (such as SEQ ID NO：1 (mRNA), NCBI Gene ID：238).
In some embodiments, the presence for being derived from RET gene rearrangement in the sample of the tumour of subject can be explained, The tumour is easily influenceed by the treatment carried out with the therapeutic agent in the group by following material composition：RET inhibitor, DP-2490, DP-3636, SU5416, BAY43-9006, BAY 73-4506 (Rui Gefeini), ZD6474, NVP-AST487, rope La Feini, RPI-1, XL184, ZD6474, Sutent, Imatinib, pazopanib, Axitinib, Mo Tesaini, Ji Fei For Buddhist nun and withaferin A (see, e.g., Samadi etc., Surgery 2010148:1228-36；Cuccuru etc., JNCI 200413:1006-1014；Akeno-Stuart etc., Cancer Research 200767:6956；Grazma etc., J Clin Oncol 201028:15s 5559；Mologni etc., J Mol Endocrinol 200637:199-212；Calmomagno etc., Journal NCI 200698:326-334；Mologni.Curr Med Chem 201118:162-175；And WO 06/ 034833rd, the compound disclosed in U.S. Patent Publication 2011/0201598 and United States Patent (USP) 8,067,434).With the side of reference Above-mentioned all bibliography are integrally incorporated herein by formula.RET inhibitor may include the expression for reducing RET or part thereof and/or swash Any reagent of enzymatic activity, including for example, reduce RET or part thereof expression and/or the oligonucleotides of activity, small molecule and/ Or peptide." (rearranged during transfection) is reset in transfection " used herein or " RET " refer to that calcium is adhered The receptor tyrosine kinase of superfamily protein, it participates in impaired neural crest development and identifies glial cell-line derived neurotrophy Factor family signaling molecule.The RET genes of many species and mRNA nucleotide sequence are known, including people (such as SEQ ID NO：3-SEQ ID NO：4 (mRNA), NCBI Gene ID：5979).
The further non-limiting examples of the application of methods described herein include detection hematologic malignancies mark (hematological malignancy) and its group (panels) (e.g., including detect gene in lymthoma and leukaemia The mark group that group is reset), the related genome rearrangement of detection sarcoma and its group and detection for lymthoma test IGH/ Tcr gene is reset and its group.
In some embodiments, method described herein is related to suffers from or is diagnosed as to have with treatment of cancer to treat Such as the subject of cancer.Subject with cancer can be identified by doctor using the method for current diagnosis cancer.For example, table It is it is known in the art that including but is not limited to levy these illnesss and contribute to the Lung Cancer Symptoms of diagnosis and/or complication：Breathe micro- There are voiced sound (dullness) and chest when weak, clavicle above enlargement of lymph nodes, pulmonary abnormalities sound, tapping (tapped) chest Portion's pain.The test that can help to diagnose such as lung cancer includes but is not limited to X ray, to high-level predetermined substance (for example, calcium) Blood testing, CT scan and tumor biopsy.Lung cancer family's medical history or exposed to lung-cancer-risk factor (for example, smoking or exposure In smog and/or air pollution) it can also contribute to determine whether subject may suffer from lung cancer or carry out pulmonary cancer diagnosis.
Cancer may include but be not limited to：Cancer (carcinoma), including gland cancer, lymthoma, blastoma, melanoma, meat Knurl, leukaemia, squamous cell carcinoma, ED-SCLC, non-small cell lung cancer, human primary gastrointestinal cancers, hodgkin's lymphomas and non-Hodgkin's Lymphomas, cancer of pancreas, glioblastoma, basal-cell carcinoma, cancer of bile ducts, carcinoma of urinary bladder, the cancer of the brain (including glioblastoma and Medulloblastoma)；Breast cancer, cervix cancer, choriocarcinoma；Colon cancer, colorectal cancer, endometrial epithelium cancer (endometrial carcinoma), carcinoma of endometrium (endometrial cancer)；Cancer of the esophagus, stomach cancer；Various incidences Cancer, intraepithelial tumor (including Bowen diseases and osteitis deformans)；Neoplastic hematologic disorder (including acute lymphatic leukemia and urgency Property myelocytic leukemia)；Kaposi's sarcoma, hairy cell leukemia；Chronic granulocytic leukemia (myelogenous Leukemia), leukaemia related AIDS and adult T-cell leukemia-lymphoma；Kidney (such as clear-cell carcinoma), T cell is acute Lymphoblastic leukemia/lymthoma, lymthoma (including Hodgkin's disease and lymphocytic lymphoma)；Liver cancer (such as liver cancer And hepatoma), Merkel cell cancers, melanoma, Huppert's disease；Neuroblastoma；Carcinoma of mouth (including squamous is thin Born of the same parents' cancer)；Oophoroma (including oophoroma as caused by epithelial cell), sarcoma (including leiomyosarcoma, rhabdomyosarcoma, fat Sarcoma, fibrosarcoma and osteosarcoma)；Cancer of pancreas；Cutaneum carcinoma (including melanoma, stroma cell, reproduction cell and mesenchyma are thin Born of the same parents)；Prostate cancer, the carcinoma of the rectum；Carcinoma of vulva, kidney (including gland cancer)；Carcinoma of testis (including embryo tumour (such as seminoma), Nonseminoma (teratoma, choriocarcinoma), mesenchymoma and germinoma)；Thyroid cancer (including thyroid adenocarcinoma and Medullary thyroid cancer)；Cancer of the esophagus, salivary-gland carcinoma and WilmShi tumours.In some embodiments, cancer can be lung cancer.
In some embodiments, method described herein includes giving the combination as described herein of effective dose to subject Thing (for example, treatment of cancer), to mitigate cancer symptoms." mitigation cancer symptoms " used herein are related to cancer to improve Any illness or symptom.Control is not treated compared to equivalent, be reduced at least 5% as such measured by any standard technique, 10%th, 20%, 40%, 50%, 60%, 80%, 90%, 95%, 99% or more.Composition described herein is given to subject Various means be known to those skilled in the art.Such method may include but be not limited to oral administration, parenteral Administration, intravenous administration, intramuscular administration, subcutaneous administration, percutaneous dosing, air flue (aerosol) administration, pulmonary administration, skin are given Medicine, local administration, drug administration by injection or intratumoral administration.Administration can be local or whole body.Term as used herein " has Effect amount " refers to mitigate the amount of the therapeutic agent needed at least one above symptom of disease or illness, and needed for being related to and being enough to provide The amount of the pharmaceutical composition of effect.Therefore, term " therapeutically effective amount " refers to be enough as the person that gives exemplary subject to produce specific The amount of anticancer effect.Effective dose used herein can also cover in different contexts to be enough to delay what disease symptomses developed Measure, be enough to change the amount or reverse disease symptom of disease symptomses process (such as, but not limited to, slowing down disease symptomses progress) Amount.It is therefore intended that accurate " effective dose " is typically unpractiaca.However, for any given situation, appropriate " effective dose " Normal experiment can be used only by those of ordinary skill in the art to determine.The effect of any given dose can pass through suitable biology Measure is monitored.Dosage can be determined by doctor, and can be adjusted when necessary to adapt to observed therapeutic effect.
The non-limiting examples for the treatment of of cancer may include radiotherapy, surgical operation, gemcitabine, cis-platinum (cisplastin), taxol, carboplatin, bortezomib, AMG479, Vorinostat (vorinostat), Rituximab (rituximab), Temozolomide (temozolomide), rapamycin, ABT-737, PI-103；Alkylating agent, such as thiotepa (thiotepa) andEndoxan；Alkylsulfonate, such as busulfan, Improsulfan and A-20968 (piposulfan)；Aziridine (aziridines), for example, benzodopa, carboquone (carboquone), meturedopa and uredopa；Aziridine (ethylenimines) and methylamelamines, including hemel, triethylenemelamine (triethylenemelamine), triethylene phosphoramide (TEPA) (trietylenephosphoramide), thio triethylene phosphoramide (TEPA) And trimethylolomelamine (triethiylenethiophosphoramide)；Acetogenin (acetogenins) (particularly bullatacin (bullatacin) and bullatacinone)；Camptothecine (including synthetic analogues Hycamtin)；Tongue Moss chalone (bryostatin)；callystatin；CC-1065 (including its Adozelesin (adozelesin), Carzelesin (carzelesin) and Bizelesin (bizelesin) synthetic analogues)；Nostoc element (cryptophycins) (is particularly read Pearl algae element 1 and nostoc element 8)；Dolastatin；Duocarmycin (including synthetic analogues, KW-2189 and CB1-TM1)； eleutherobin；pancratistatin；sarcodictyin；Halichondrins (spongistatin)；Mustargen (nitrogen ), such as Chlorambucil, Chlornaphazine, cholophosphamide, estramustine, ifosfamide, dichloromethyl two mustards Ethamine, mustargen oxide hydrochloride, melphalan, novembichin (novembichin), phenesterin (phenesterine), Pennisetum mustard (prednimustine), trofosfamide (trofosfamide), uracil mastard；Nitroso ureas, such as block Mo Siting, chloramphenicol (chlorozotocin), Fotemustine (fotemustine), lomustine (lomustine), Buddhist nun are not Take charge of spit of fland (nimustine) and ranimnustine；Antibiotic, such as enediyne (enediyne) antibiotic (such as calicheamicin (calicheamicin), particularly khaki mycin γ 1I and calicheamicin Ω I1 (see, for example, Agnew, Chem.Intl.Ed.Engl., 33：183-186(1994))；Dynemicin, including dynemicin A；Diphosphonate , such as chlorophosphate (clodronate) (bisphosphonates)；Ai Sipeila mycins (esperamicin)；And brand-new Cancer rhzomorph chromophore and related chromoprotein enediyne antibiotic chromophore), aclacinomysins, D actinomycin D, Authramycin, azaserine, bleomycin, cactinomycin, carabicin, caminomycin, carzinophillin (carzinophilin), chromomycinis, dactinomycin D, daunorubicin, detorubicin, 6- diazonium -5- oxos-L- Nor-leucine,Adriamycin (including morpholino adriamycin, cyanines base morpholino adriamycin, 2- pyrrolins- Adriamycin and deoxy doxorubicin), Epi-ADM, esorubicin (esorubicin), idarubicin, marcellomycin (marcellomycin), mitomycin (such as mitomycin C), Mycophenolic Acid, nogalamycin (nogalamycin), olive is mould Plain (olivomycins), Peplomycin (peplomycin), potfiromycin, puromycin, triferricdoxorubicin (quelamycin), rodorubicin (rodorubicin), streptonigrin, streptozotocin, tubercidin, ubenimex, net department His fourth (zinostatin), zorubicin (zorubicin)；Antimetabolite, such as methotrexate (MTX) and 5 FU 5 fluorouracil (5-FU)； Folacin, such as two chrysomelid sour (denopterin), methotrexate (MTX), pteropterin and Trimetrexate；Purine analogue, such as Fludarabine (fludarabine), Ismipur, thiamiprine, thioguanine；Pyrimidine analogue, such as ancitabine (ancitabine), azacitidine, 6- aza uridines (azauridine), Carmofur (carmofur), cytarabine (cytarabine), di-deoxyuridine (dideoxyuridine), doxifluridine, enocitabine, floxuridine；Androgen, example Such as Calusterone (calusterone), Masterone, epithioandrostanol, Mepitiostane (mepitiostane), Testolactone； Anti- adrenal gland, such as aminoglutethimide (aminoglutethimide), mitotane (mitotane), Trilostane；Folic acid supplements Agent, such as folinic acid (frolinic acid)；Second glucurolactone；Aldophosphamideglycoside (aldophosphamide glycoside)；Amino-laevulic acid；Eniluracil (eniluracil)；Amsacrine；bestrabucil；Bisantrene (bisantrene)；edatraxate；defofamine；Demecolcine (demecolcine)；Aziridinyl Benzoquinone (diaziquone)； elformithine；Elliptinium Acetate；Epothilones；Ethoglucid (etoglucid)；Gallium nitrate；Hydroxycarbamide；Lentinan； lonidainine；Maytansinoid (maytansinoids), such as maytansine (maytansine) and ansamitocin (ansamitocins)；Mitoguazone (mitoguazone)；Mitoxantrone；mopidanmol；nitraerine；Pentostatin； Benzene comes U.S. special (phenamet)；THP；Losoxantrone；podophyllinic acid；2-ethylhydrazide；Third card Bar hydrazine；Polysaccharide compound (JHS Natural Products, Eugene, Oreg.)；Tetrahydroform (razoxane)；Root Knurl rhzomorph；sizofuran；Spiro germanium (spirogermanium)；Tenuazonic acid (tenuazonic acid)；Sanya Amine quinone (triaziquone)；2,2',2″-trichlorotriethylamine；Trichothecenes (trichothecenes) (particularly T-2 toxin, verracurin A, myrothecin A (roridin A) and anguidin (anguidine))；Amino first Acetoacetic ester (urethan)；Eldisine；Dacarbazine；Mannomustin；Dibromannitol (mitobronitol)；Dibromo is defended Lance alcohol (mitolactol)；Pipobroman (pipobroman)；gacytosine；Arabinoside (" Ara-C ")；Ring phosphinylidyne Amine；Thiotepa；Taxanes, such asTaxol (Bristol-Myers Squibb Oncology, Princeton, N.J.),Cremophor-free, taxol albumin engineering nanoparticle formulations (American Pharmaceutical Partners, Schaumberg, Ill.) anddoxetaxel (Rhone-Poulenc Rorer, Antony, France)；Chlorambucil (chloranbucil)；Ji Xi His shore；6- thioguanines；Purinethol；Methotrexate (MTX)；Platinum analogs, such as cis-platinum, oxaliplatin and carboplatin；Vinblastine； Platinum；Etoposide (VP-16)；Ifosfamide；Mitoxantrone；Vincristine；NAVELBINE.RTM. vinorelbine；Novantrone (novantrone)；Teniposide；Edatrexate；Daunorubicin；Aminopterin-induced syndrome；Xeloda (xeloda)；Ibandronate (ibandronate)；Irinotecan (Camptosar, CPT-11) (including Irinotecan and 5-FU and formyl tetrahydrofolic acid are controlled Treatment scheme)；Topoisomerase enzyme inhibitor RFS2000；DFMO (DMFO)；Retinoids, such as retinoic acid；Card training His shore；Combretastatin (combretastatin)；Formyl tetrahydrofolic acid (LV)；Oxaliplatin, including oxaliplatin therapeutic regimen (FOLFOX)；Lapatinib (Tykerb.RTM)；PKC- α, Raf, H-Ras, EGFR are (for example, Tarceva) With VEGF-A inhibitor (reducing cell propagation), and the pharmaceutically acceptable salt of any of the above material, acid or derivative. In addition, treatment method can further comprise using radiation-therapy or radiotherapy.In addition, treatment method can further comprise using Surgical operation therapy.
In some embodiments, method described herein is applicable to resurvey sequence (resequencing), for example, with In it is determined that the sequence of the especially relevant of acquisition, low quality and/or complexity is sequenced by the non-directional of a large amount of nucleic acid.With non-limiting The mode of example, method described herein can allow to the orientation of targeting disease genome (for example, 10-100 gene) and/or Targeting resurveys sequence, resurveys sequence to determine the variant, full extron group (whole exome) weight that are obtained in large scale sequencing project It is sequenced, and/or is made a variation for detecting monokaryon sweet acid, polynucleotides makes a variation, insert, delete, copy number changes and the shape that methylates Sequence is resurveyed in the targeting of state.
In some embodiments, method described herein can allow micropopulation (microbiota) sequencing, ancient times sample Product (ancient sample) are sequenced, and/or new variant gene typing.
For description and disclosed purpose, herein by reference by the application in the whole text cited all patents and its Its publication (including bibliography, granted patent, disclosed patent application and common pending (co-pending) patent Shen Please) it is expressly incorporated herein, such as the methodology available for technology described herein described in such publication.These are published Thing is only because their disclosure provides earlier than the applying date of the application.It is not construed as recognizing the present inventor in this regard There is no right to shift to an earlier date disclosure by means of previous invention or because of any other reason.These all about files The statement on date or the statement of content of these files be to be based on the available information of applicant, do not form on these files Date or any of correctness of content of these files recognize.
Description to embodiment of the present disclosure is not intended to be exhaustive or the disclosure is limited in into exact form disclosed. Although the embodiment and embodiment of the disclosure are described for purpose of explanation herein, those skilled in the art will , it will be recognized that a variety of equivalent modifications can be made in the range of the disclosure.Although for example, by method and step or function with given order Provide, other embodiment can be implemented function or can substantially simultaneously be implemented these functions with different order.Carried herein The teaching of the disclosure of confession can be applied to other programs or method by rights.Can be by various embodiments described herein It is combined to provide further embodiment.If needed, can to the disclosure in terms of modify, with utilize above-mentioned ginseng Composition, function and design in examining and applying, to provide disclosure further embodiment.Can according to be described in detail come Above-mentioned change and other changes are carried out to the disclosure.All such modifications both fall within the present invention that appended claims are limited Within the scope of.
Key element in any aforementioned embodiments can be combined or substitute the key element in other embodiment.This Outside, it is other although the advantage related to the particular implementation of the disclosure is described in the context of these embodiments Embodiment can also show such advantage, but not all embodiment must all show such advantage, can just fall into this Scope of disclosure.
The techniques described herein are further explained by following examples, but should in no way be interpreted as skill as described herein Art is further limited.
Some embodiments of technology described herein can be defined according to any following numbering paragraph：
1. a kind of method determined with the nucleotide sequence of known target nucleotide sequences adjoining, methods described include：
(a) target nucleic acid comprising the known target nucleotide sequences is connected with general oligonucleotide pigtail connection；
(b) part for the target nucleic acid and the general widow are expanded with the first adapter-primer and the first target specific primer The amplification chain of nucleotides pigtail connection；
(c) part for the amplicon as caused by step (b) is expanded with the second adapter-primer and the second target specific primer；
(d) the amplification part caused by step (c) is sequenced using the first sequencing primer and the second sequencing primer；
Wherein, the general oligonucleotide pigtail connection, which includes first, can connect duplex ends and the second unpaired end；
Wherein, the general oligonucleotide pigtail connection includes sealed joint and amplification chain；
Wherein, the sealed joint includes 5 ' double stranded sections；
Wherein, the amplification chain includes unpaired 5 ' parts, 3 ' double stranded sections and 3 ' T and protruded；
Wherein, the amplification chain includes and the first sequencing primer and the second sequencing primer identical nucleotide sequence；
Wherein, the double stranded section of the sealed joint and the amplification chain is substantially complementary, and forms the institute protruded comprising 3 ' T Duplex ends can be connected by stating first；
Wherein, the double stranded section long enough, to maintain double chain form at a temperature of connection；
Wherein, first target specific primer, which includes, specificity to be annealed to the institute of the target nucleic acid at an annealing temperature State the nucleotide sequence of known target nucleotide sequences；
Wherein, second target specific primer includes 3 ' and partly partly moved back with 5 ' parts, described 3 ' containing energy specificity The nucleotide sequence of a part for the known target nucleotide sequences that fire to the amplicon as caused by step (b) is included, it is described 5 ' partly contain with the second sequencing primer identical nucleotide sequence, and second target specific primer is relative to described first Target specific primer is nested；
Wherein, first adapter-primer includes 5 ' the part identical nucleotide sequences with first sequencing primer；With And
Wherein, second adapter-primer includes a part of identical nucleotide sequence with first sequencing primer, and It is and nested relative to first adapter-primer.
2. the method as described in section 1, wherein, the sealed joint of the general oligonucleotide pigtail connection further includes 3 ' unpaired parts, 3 ' the unpaired part substantially not with it is described amplification chain described 5 ' unpaired partial complementarities；And
Wherein, described 3 ' unpaired parts of the sealed joint are or substantially different substantially not with any Primers complementary In any primer.
3. such as the method any one of section 1-2, wherein, second adapter-primer passes through at least three nucleotides phase It is nested for first adapter-primer.
4. such as the method any one of section 1-3, wherein, containing with first sequencing primer and second sequencing The part of the amplification chain of primer identical nucleotide sequence is at least partly contained in described 5 ' unpaired portions of the amplification chain Point.
5. such as the method any one of section 1-4, wherein, first target specific primer further includes 5 ' labels Sequence, 5 ' the sequence label part include substantially not with any other partial complementarity of any primer or substantially not It is same as the nucleotide sequence of the high GC content of any other part of any primer.
6. such as the method any one of section 1-5, wherein, second adapter-primer and total length the first sequencing primer phase Together.
7. such as the method any one of section 1-6, wherein, specificity is annealed to the target specific primer of known target Part will in PCR buffer solutions at a temperature of about 65 DEG C specificity annealing.
8. such as the method any one of section 1-7, wherein, methods described further includes as follows before step (a) Step：
Mechanical shearing is carried out to the nucleic acid；
Repair the nucleic acid experience end；
Make the nucleic acid experience phosphorylation；
And make the nucleic acid experience polyadenylation.
9. such as the method any one of section 1-8, wherein, the sample includes genomic DNA.
10. such as the method any one of section 1-9, wherein, the sample includes RNA, and methods described is further First step including making the sample experience reverse transcriptase scheme.
11. such as the method any one of section 1-10, wherein, the reverse transcriptase scheme is poly- including the use of random six Body.
12. such as the method any one of section 1-11, it is known that target sequence is contained in gene rearrangement.
13. the method as described in section 12, wherein, the gene rearrangement is present in selected from the group being made up of following material In nucleic acid：
Genomic DNA, RNA and cDNA.
14. such as the method any one of section 12-13, wherein, the gene rearrangement includes oncogene.
15. the method as described in section 14, wherein, the gene rearrangement includes fusion oncogene.
16. such as the method any one of section 1-15, wherein, nucleic acid product is surveyed by PCR sequencing PCR of future generation Sequence.
17. the method as described in section 16, wherein, the PCR sequencing PCR of future generation includes being selected from what is be made up of following methods Method in group：
Ion Torrent, Illumina, SOLiD, 454, extensive parallel signature sequencing, the reversible Dye Terminator thing of solid phase Sequencing and the sequencing of DNA nanospheres.
18. such as the method any one of section 1-17, wherein, first sequencing primer and second sequencing primer PCR sequencing PCR of future generation selected by compatibility.
19. such as the method any one of section 1-18, wherein, methods described is included the sample or the sample Unitary part contacts with multigroup first target specific primer and the second target specific primer.
20. such as the method any one of section 1-19, wherein, methods described include will be comprising the sample it is single anti- Mixture is answered to be contacted with multigroup first target specific primer and the second target specific primer.
21. such as the method any one of section 1-20, wherein, multigroup first target specific primer and the second target are special Specific primer specificity is annealed to the known target nucleotide sequences included by different genes.
22. such as the method any one of section 1-21, wherein, at least two group of first target specific primer and the second target are special Specific primer specificity is annealed to the different piece of known target nucleotide sequences.
23. such as the method any one of section 1-22, wherein, at least two group of first target specific primer and the second target are special Specific primer specificity is annealed to the different piece of the individual gene containing known target nucleotide sequences.
24. such as the method any one of section 1-23, wherein, at least two group of first target specific primer and the second target are special Specific primer specificity is annealed to the different extrons of the gene containing known target nucleotide sequences.
25. such as the method any one of section 19-24, wherein, multiple first target specific primers include identical 5 ' Sequence label part.
26. such as the method any one of section 1-25, wherein, the general oligonucleotide pigtail connection further includes Bar code part.
27. the method as described in section 26, wherein, by several samples each with the general few core with unique bar code part Thuja acid pigtail connection contacts；And wherein, the sample is merged after step (a).
28. such as the method any one of section 1-27, wherein, each amplification step includes length and is 5 circulating -20 The PCR amplification scheme circulation groups of circulation.
29. such as the method any one of section 1-28, wherein, the target specific primer and the adapter-primer are set Count into specific can be annealed to their complementary series under about 61-72 DEG C of annealing temperature.
30. such as the method any one of section 1-29, wherein, the target specific primer and the adapter-primer are set Count into specific can be annealed to their complementary series under about 65 DEG C of annealing temperature.
31. such as the method any one of section 1-30, wherein, the sample includes the biological sample for being derived from subject Product.
32. such as the method any one of section 1-31, wherein, the sample is derived from needs and treated and hereditary change phase The subject of the disease of pass.
33. the method as described in section 32, wherein, the disease is cancer.
34. such as the method any one of section 1-33, wherein, the sample includes tumor cell group.
35. such as the method any one of section 1-34, wherein, the sample includes tumor biopsies section.
36. such as the method any one of section 1-35, wherein, the cancer is lung cancer.
37. such as the method any one of section 1-36, wherein, the known target sequence is contained in disease related gene In.
38. such as the method any one of section 1-37, wherein, the known target sequence is contained in the gene weight in sample In scheduling thing.
39. such as the method any one of section 1-38, wherein, the gene rearrangement product is oncogene.
40. such as the method any one of section 1-39, wherein, the known target sequence is included from being selected from following gene Group in gene sequence：
ALK, ROS1 and RET.
41. the method as described in section 40, wherein, at least one set of first target specific primer and the second target specific primer choosing From in the group being made up of following primer：
SEQ ID NO：5 and SEQ ID NO：6；SEQ ID NO：7 and SEQ ID NO：8；SEQ ID NO：9 and SEQ ID NO：10；SEQ ID NO：11 and SEQ ID NO：12；SEQ ID NO：13 and SEQ ID NO：14；SEQ ID NO：15 and SEQ ID NO：16；SEQ ID NO：17 and SEQ ID NO：18；SEQ ID NO：19 and SEQ ID NO：20；SEQ ID NO：21 Hes SEQ ID NO：22；SEQ ID NO：23 and SEQ ID NO：24；SEQ ID NO：25 and SEQ ID NO：26；SEQ ID NO： 27 and SEQ ID NO：28；SEQ ID NO：29 and SEQ ID NO：30；SEQ ID NO：31 and SEQ ID NO：32；SEQ ID NO：33 and SEQ ID NO：34；SEQ ID NO：35 and SEQ ID NO：36；And SEQ ID NO：37 and SEQ ID NO： 38。
42. such as the method any one of section 40-41, wherein, the ALK in the sample obtained from the tumour of subject The presence of gene rearrangement illustrates that the tumour is easily treated by what is carried out with the therapeutic agent in the group by following material composition Influence：
ALK inhibitor, gram azoles for Buddhist nun (PF-02341066), AP26113, LDK378,3-39, AF802, IPI-504, ASP3026, AP-26113, X-396, GSK-1838705A, CH5424802 and NVP-TAE684.
43. such as the method any one of section 40-41, wherein, the ROS1 in the sample obtained from the tumour of subject Gene rearrangement presence illustrate the tumour easily by with the group by following material composition therapeutic agent carry out controlling The influence for the treatment of：
ROS inhibitor, ALK inhibitor, gram azoles for Buddhist nun (PF-02341066), AP26113, LDK378,3-39, AF802, IPI-504, ASP3026, AP-26113, X-396, GSK-1838705A, CH5424802 and NVP-TAE684.
44. such as the method any one of section 40-41, wherein, the RET in the sample obtained from the tumour of subject The presence of gene rearrangement illustrates that the tumour is easily treated by what is carried out with the therapeutic agent in the group by following material composition Influence：
RET inhibitor, DP-2490, DP-3636, SU5416, BAY 43-9006, BAY73-4506 (Rui Gefeini), ZD6474, NVP-AST487, Sorafenib, RPI-1, XL184, ZD6474, Sutent, Imatinib, pazopanib, Ah Replace Buddhist nun, Mo Tesaini, Gefitinib and withaferin A in west.
45. a kind of method for the treatment of cancer, methods described include：
According to the method any one of section 1-44, to being derived from the tumor sample for the subject for needing treating cancer The presence that more than one oncogenes are reset is detected；
Give the effective treatment of cancer of tumour for being reset with any oncogene detected.
46. such as method of section 45, wherein, the therapeutic agent in the group by following material composition is for ALK cancers The tumour of gene rearrangement is effective：
ALK inhibitor, gram azoles for Buddhist nun (PF-02341066), AP26113, LDK378,3-39, AF802, IPI-504, ASP3026, AP-26113, X-396, GSK-1838705A, CH5424802 and NVP-TAE684.
47. the method as described in section 45, wherein, therapeutic agent in the group by following material composition for The tumour that ROS1 oncogenes are reset is effective：
ROS1 inhibitor, ALK inhibitor, gram azoles for Buddhist nun (PF-02341066), AP26113, LDK378,3-39, AF802, IPI-504, ASP3026, AP-26113, X-396, GSK-1838705A, CH5424802 and NVP-TAE684.
48. the method as described in section 45, wherein, therapeutic agent in the group by following material composition for The tumour that RET oncogenes are reset is effective：
RET inhibitor, DP-2490, DP-3636, SU5416, BAY 43-9006, BAY73-4506 (Rui Gefeini), ZD6474, NVP-AST487, Sorafenib, RPI-1, XL184, ZD6474, Sutent, Imatinib, pazopanib, Ah Replace Buddhist nun, Mo Tesaini, Gefitinib and withaferin A in west.
49. a kind of determine needs whether the subject for the treatment of cancer can treat the method that respond, the side to given Method includes：
According to the method any one of section 1-44, reset to being derived from oncogene in the tumor sample of the subject Presence detected；
Wherein, reset if detecting the presence of the oncogene, determine the subject to targetting oncogene rearrangement product Treatment respond.
50. the method as described in section 49, wherein, if detecting the presence of the rearrangement of ALK oncogenes, the subject can be to choosing Responded from the therapeutic agent in the group being made up of following material：
ALK inhibitor, gram azoles for Buddhist nun (PF-02341066), AP26113, LDK378,3-39, AF802, IPI-504, ASP3026, AP-26113, X-396, GSK-1838705A, CH5424802 and NVP-TAE684.
51. the method as described in section 49, wherein, if detecting the presence of the rearrangement of ROS1 oncogenes, the subject can be right Therapeutic agent in the group being made up of following material responds：
ALK inhibitor, gram azoles for Buddhist nun (PF-02341066), AP26113, LDK378,3-39, AF802, IPI-504, ASP3026, AP-26113, X-396, GSK-1838705A, CH5424802 and NVP-TAE684.
52. the method as described in section 49, wherein, if detecting the presence of the rearrangement of RET oncogenes, the subject can be to choosing Responded from the therapeutic agent in the group being made up of following material：
RET inhibitor, DP-2490, DP-3636, SU5416, BAY 43-9006, BAY73-4506 (Rui Gefeini), ZD6474, NVP-AST487, Sorafenib, RPI-1, XL184, ZD6474, Sutent, Imatinib, pazopanib, Ah Replace Buddhist nun, Mo Tesaini, Gefitinib and withaferin A in west.
53. such as the method any one of section 44-52, wherein, the cancer is lung cancer.
Embodiment
Embodiment 1
In one embodiment, described herein used from fresh sample or formalin is fixed and FFPE (FFPE) analysis that the RNA of sample or genomic DNA are carried out as template, the analysis, which uses, is used for sequencing library of future generation structure New half truncate Y-shaped joint, after to carry out two single end nested-polymerase chain reaction (single-end nested Polymerase chain reactions), rapidly and effectively target enrichment can be realized.The enrichment method, which can be realized, to be used for Sequence is resurveyed in the cDNA or gDNA of the potential following situation of detection targeting：Hereditary change (single nucleotide variations, insertion deletion, with And copy number), epigenetic change (methylating), gene expression and genome rearrangement.
It is sequenced compared to full-length genome, full extron group and full transcript profile, the target enrichment before next generation's sequencing has more cost Benefit, therefore be more suitable for finding in research and being widely implemented in clinical practice.The high overburden depth energy provided by target enrichment method It is enough to realize that the allele compared with wide dynamic range counts (in gene expression and copy number are assessed) and the inspection to low frequency mutation Survey and (be used for the key feature for evaluating the somatic mutation in cancer).In the extensive of genome sequencing or full sequencing of extron group Be implemented as may before, the main flow of clinical of future generation sequencing will be related to the disease of gene target of the selection with discrete number Group.Equally, the investigation of the gene target analysis large sample size based on determination is also required to the genotyping approach of economy.Herein Described analysis will be applied to both of these case.
For the detection reset in chromosome again arrangement and chromosome, genome sequencing or the sequencing of full transcript profile are to new base Because group discovery reset is useful, and involved gene/chromosome companion need not be known a priori by.However, these full genomes Prescription method and full transcript profile method are because cost is high, depth is low causes poor sensitivity and to bioinformatic analysis for sequencing It is required that it is high, it is at present in clinical setting and impracticable.FISH (FISH) is always clinically to detect genome rearrangement Goldstandard analysis；However, the analysis is small throughput, and its implementation needs special equipment and professional knowledge/experience. RT-PCR is also effective in such rearrangement is detected, but RT-PCR needs to know 5 ' companions and 3 ' companions, and not can be extended to big Measure target/sample.
The example of the conventional preparation enrichment analysis of next generation's sequencing includes：Capture analysis (TruSeq based on hybridization Capture, Illumina；SureSelect Hybrid Capture, Agilent) and based on PCR (PCR) Analysis (HaloPlex, Agilent；AmpliSeq, Ion Torrent；TruSeq Amplicon, Illumina；Emulsion/number Word PCR, Raindance).Method based on hybridization not only captures the targeting sequence of captured probe covering, also captures Consume the base of missing the target near extra sequencing ability.In addition, these methods are all relatively time-consuming, labour intensive and specifically compared with It is low.The method of PCR-based amplification more simply and faster, but needs the forward direction positioned at target gene seat both wings to draw according to conventional design Thing and reverse primer.Especially, for detecting the genome rearrangement with unknown fusion partner, PCR is inapplicable.
As described herein is to use the target enrichment point for being used for the new half truncation Y-shaped joint that sequencing library of future generation is built The cDNA from fresh sample or FFPE samples or gDNA quickly can be sequenced for analysis, the analysis.Fig. 1 is for Ion The library construction for target enrichment is summarised exemplified by half truncation Y-shaped connector of Torrent sequencings.Importantly, this method is applicable In any other microarray dataset of future generation, including but not limited to Illumina, SOLiD and 454.In short, can be to random shearing Double-strand cDNA or gDNA template carry out end reparation, polyadenylation, then the connection universal Y on one or two ends of end Joint, so as to which the universal sequence for originating PCR and being subsequently sequenced be made.The use of first round PCR is marked with filling afterbody (stuffer tail) (it is described filling afterbody contribute to be multiplexed (multiplexing) a large amount of targets) target specific primer and The 20 base identical primers protruded with 5 ' Y-shaped connectors.Second wheel PCR is carried out with following primer：30 protruded with 5 ' Y-shaped connectors Base identical primer；Target-specific nested with second series connection (tandem) in the 3 ' downstreams for being annealed to the first target specific primer Primer.Depending on sequencing technologies, the second series connection nested primers is marked with downstream emulsion-based PCR or cluster 5 ' (clustering) the second primer sequence needed for.By the way that by target sequence more than 36-40 base of effective covering, (this is depended on Interval between primer) unidirectional series connection nested primers (unidirectional tandem, nested primers), make this System obtains high specific.It is worth noting that, PCR cycle number can according to the initial nucleic acid material used number, merge The quantity of sample and the quantity of target optimize.
Sum it up, this method truncates Y-shaped connector using half uniformly marks all dsDNA fragments with 3 ' common ends, should 3 ' common ends are used in the two-wheeled PCR using two One-way nesting target specific primers progress to obtain specificity.Band The application of the nested primers of label also avoid the primer same two during many different locis in target gene group or transcript profile Dimerization and the influence of heterodimerization.In addition to being multiplexed target, method described herein also allows after Y-shaped connector connects (step 2) Merge multiple sample, during this period, single sample is connected with the bar code joint of uniqueness.Once added by Y-shaped connector connection Bar code, multiple samples can be incorporated into a reaction tube and be used for downstream target enrichment.
With the detection to genome rearrangement (to inserting and deleting sequencing mistake (for example, according to homopolymer result The sequencing mistake found in the sequencings of Torrent and 454) there is higher tolerance) on the contrary, to single base and more base mutations (bag Include insertion and delete) detection need can use Illumina microarray datasets realize the sequencing with higher accuracy.For this One purpose, for example, can by using be marked with Illumina forward directions joint sequence (bar coded or not bar coded) primer and Truncation 3 ' of the gene specific nested primers (GSP2 for being marked with Illumina reverse primers) of tape label to the protrusion of Y-shaped connector Arm is expanded, and will partly truncate Y-shaped connector library transformation into Illumina libraries.Similarly, also can be by the first PCR (steps Rapid 3) the middle primer using tape label introduces sequencing primer to realize two-way sequencing via the prominent Y-shaped connector of truncation 3 ' arm.
Analysis as described herein and method are applied to the cDNA of FFPE samples is derived from, by using targeting seven outside Seven gene-specific primers of aobvious son (including ROS1 kinase domains) detect to ROS1 Gene Fusions.With known Fusion partner and fusion partner unknown in the past detect ROS1 genome rearrangements, such as " SLC34A2 exons 1s 2-ROS1 Exon 34 " merges and " EZR extron 9-ROS1 exon 3s 4 " merge.The analysis realize high target-hit specificity (when When being mapped using human genome hg19 references, for~85-95%), this makes it possible to the sequencing using even smallest size Platform (therefore generally the least expensive) (such as the chips of Ion Torrent PGM 314) with high coverage result (7 target gene seats, 5 Sample, each target of each sample>1000 × coverage) multiple samples are sequenced.Fig. 2 is shown sequencing read mapping Target gene seat into gene ROS1 kinase domains.
The advantage of methods described herein includes：
1. method described herein can be used for the target enrichment of double-strand cDNA or gDNA from fresh sample or FFPE samples, Allow to map 5 ' and 3 ' two ends of target cDNA or gDNA fragment using sequencing of future generation.It is currently based on the side of hybridization Method needs a couple of days to be prepared and be hybridized, and because the sequence of missing the target near capturing is shown compared with low specificity.It is currently based on The method of amplification needs forward and reverse primer known to design, and is not suitable for the high scale multiplexing of target.
2. simple bioinformatic analysis.According to the quantity of selected target, the data as caused by the analysis are carried out Analysis is simple and efficiently.In addition, this method can be set as compatible with current existing bioinformatics tools.Therefore, Small clinical laboratory will be without great amount of investment (this will limit the extensive clinical implementation of sequencing of future generation) in bioinformatics, just Data analysis can be carried out.
3. high specific (~85-95%).Due to having left the initial gene group or transcript profile library thing of " can be sequenced " Matter, traditional Y-shaped connector construct with forward and reverse primer (5 ' and 3 ' is prominent) two kinds of components for conventional libraries structure High-caliber background is introduced into miss the target sequencing.For example, if target size is 100bp and is present in two of a genome to copy The ratio of Bei Zhong, target and genome is about 1:3×10^7.The biotinylated oligonucleotides bait of method generally use based on hybridization (baits), with target fragment pull-out of the magnetic bead by hybridization by being coated with Streptavidin.Possible 3 × 10^7 possibility In only one non-specific binding events by significantly cause 50% miss rate.Half use for truncating Y-shaped connector is effectively prevented from This background leftover problem, because start library material can not be amplified in the preparation process for being subsequently used for sequencing.Pass through Extra specificity is obtained using two unidirectional primers (GSP2 is in GSP1 3 ' downstreams).In fact, two primers of connecting Trigger (priming) site using the target for producing 40 (assuming that primers that two 20 base-pairs are grown) and compare only with a primer For relatively high specific.Total length 30-mer primers (are used as logical in the use of 5 ' 20-mer primers and the 2nd PCR in first PCR With trigger site nested primers) use further increase specificity.Finally, two are carried out by using the primer of tape label Individual PCR steps and obtain extra specificity.The primer of tape label prevents primer homodimer by the formation of intramolecular hair fastener With the increase of heterodimer, the increase of the primer homodimer and heterodimer may dominate PCR reactions, and cause non-specific Property and unwanted artifacts, therefore, the primer of tape label allows to be multiplexed multiple targets while primer dimer is avoided.
4. cost economy.Crucial composition in methods described herein is the primer of traditional unmodified tape label, mark Quasi- PCR reagent and regular thermocyclers.Unlike the catching method based on hybridization or the setting of microfluid digital pcr, the target enrichment Scheme avoids using relatively expensive biotinylated oligonucleotide, is coated with the magnetic bead and special equipment of Streptavidin.One Denier produces, GSP1 the and GSP2 primer mixtures of merging can be used for thousands of reactions.
5. automation.Because method described herein purifies dependent on standard PCR amplification techniques and SPRI, therefore exists in high pass It is easy to the possibility of automation in amount application.Volume can be adjusted for 384 orifice plates and implemented for ultra-high throughput.
The application of methods described herein and analysis includes but is not limited to：1. by known treatment target (including Gene A LK, ROS1 and RET) composition lung cancer transposition (translocation) group；2. hematologic malignancies group, including detection lymthoma and white The group of genome rearrangement in blood disease；3. sarc gene group rearrangement group；4. for the IGH/TCR gene rearrangements of lymthoma test Group；5. the targeting disease genome (10-100 gene) for resurveying sequence；6. for confirming to obtain in large scale sequencing project Sequence is resurveyed in the targeting of the variant obtained；7. the potentiality of sequence are resurveyed in full extron group targeting；8. for detecting single nucleotide variations, multinuclear Sequence is resurveyed in thuja acid variation, insertion, deletion, copy number change and the targeting of methylation state；9. micropopulation is sequenced；10. ancient times Sample is sequenced；11. new variant gene typing.
Embodiment 2：For detecting targeting next generation's sequencing analysis of ALK, ROS1 and RET gene rearrangement simultaneously
To the understanding of chromosomal rearrangement state in cancer for the targeted therapy of individuation it is extremely important.At present, retouched Three major receptors EGFR-TKs for being related to rearrangement in lung cancer are stated.The gene rearrangement for being related to ALK gene is established as Therapeutic targets.The clinical testing data of early stage is also shown that ROS1 inhibitor resets positive patient in ROS1 after tested in treatment In effectively.External evidence shows that the tumour cell for carrying RET rearrangements responds to RET inhibitor.Therefore, ALK, ROS1 and RET represents three important therapeutic targets in lung cancer at present.
Clinical analysis currently used for detecting gene rearrangement includes：FISH (FISH), immunohistochemistry And reverse transcriptase polymerase chain reaction (RT-PCR) (IHC).FISH and IHC is sentenced due to its small throughput, high cost and complexity Read that the growth to high volume test/screening requirements possibly can not be adapted to.RT-PCR analyses need fully to know two fusion partners, And this is sometimes unavailable, Clinical Sensitivity significantly affects.Multiple RT-PCR is related to known to two for detection and melted The different of different extrons are merged between closing companion.Generally, these analyses are limited to once to be directed to a gene target, and its method needs Multiple reactions are set and analysis.
Being widely used in based on the newest analysis of future generation being sequenced for sequencing will be captured for transcript profile sequencing or target Research and exploration purpose in large-scale sequencing facility.These analyses under research environment are generally obtained due to target enormous amount Low sequencing depth is obtained, so as to produce harmonic analysis sensitivity and subsequent bad Clinical Sensitivity.Although afford large-scale survey Sequence facility, but these analyses are even unavailable for many clinical labororatories.
Method and the analysis for being related to targeting sequence measurement are described above, this method and analysis use and come from fresh sample Or formalin is fixed with the RNA of the sample of FFPE (FFPE) or genomic DNA as template, is surveyed using for the next generation New the half of sequence library construction truncates Y-shaped joint, after to carry out two single end nested-polymerase chain reactions, can realize Rapidly and effectively target enrichment.
According to this method, describe to detect ALK, ROS1 and RET gene rearrangement in the present embodiment specific Analyze (Fig. 3 A- Fig. 3 B).Gene-specific primer (GSP1) is designed to trigger kinase domain nearby or on kinase domain Extron.Nested primers (GSP2) is designed in same extron and the neighbouring GSP1 matched with them triggers GSP1's Downstream.Group includes being used for seven pairs of primers for targetting ROS1 exon 3s 1-37 at present；For targetting ALK exons 1s 9-22 4 couple Primer；And for targetting RET extrons 8-13 6 pairs of primers.
The analysis, can by using the platform specific linkers sequence after half functionalization " Y " joint design and GSP2 primers Suitable for different NGS microarray datasets.After sequencing, read is mapped into human genome reference, enabling use is by the present inventor The bioinformatics of exploitation come identify the reading frame state of fusion partner gene, alternative splicing and fusion (for example, Fig. 4 A and Fig. 4 B).Gained output is the simple note table (Fig. 4 C) for fast report.Using bar coded with Multi-example These three gene target group analysis, operation is sequenced using an Ion Torrent and detected ROS1, ALK and RET rearrangement positive Sample.
The analysis is applicable to the RNA of degraded, is carried for example, being fixed from formalin in the sample with FFPE (FFPE) The RNA taken, the sample are the clinical materials being most easy to get extensively in molecule diagnostic test.Desk-top (bench-top) is used in the analysis NGS platforms (a kind of simple bioinformatics analysis pipeline), therefore relatively easily implement in clinical labororatory.It is noticeable It is that the analysis need not be known a priori by fusion partner, and can be in the detection various bases related to main (principle) target gene Because obtaining high Clinical Sensitivity in companion's (and corresponding multiple extrons).In addition, if one of companion is known, the analysis It is also effective for 5 ' unknown fused upstream companions or unknown 3 ' downstream fusion partners.Multiplexing and deep sequencing allow pair Sample with low tumour cell composition, rare fusion and rare alternative splicing events is tested.There is provided by this analysis The rearrangement information detailed, patient is special will be useful to evaluation Genotyping specific treatment response, perhaps evaluation is used for micro- The patient-specific tumor markers of small Residual Disease monitoring is useful.Based on conventional oligonucleotide synthetic agent, finished product enzyme, Yi Ji The ability of multiple samples is multiplexed in once running, this analysis there will be the cost-benefit clinical analysis for detecting gene rearrangement.
Table 1：It is adapted to the primer (v1) of IonTorrent platforms.Primer is pointed out to include the target of known target nucleotide sequences Gene and target gene extron.R1 represents the first target specific primer, and R2 represents the second target specific primer.It is detailed in the table Information is to draw for one group of first target specificity primer of each extron listed by each gene and the second target-specific Thing.

Claims (48)

1. a kind of method determined with the nucleotide sequence of known target nucleotide sequences adjoining, methods described include：
(a) target nucleic acid comprising the known target nucleotide sequences is connected with general oligonucleotide pigtail connection；
(b) part for the target nucleic acid and the generic oligonucleotide are expanded with the first adapter-primer and the first target specific primer The amplification chain of sour pigtail connection；
(c) part for the amplicon as caused by step (b) is expanded with the second adapter-primer and the second target specific primer；
(d) the amplification part caused by step (c) is sequenced using the first sequencing primer and the second sequencing primer；
Wherein, the general oligonucleotide pigtail connection, which includes first, can connect duplex ends and the second unpaired end；
Wherein, the general oligonucleotide pigtail connection includes sealed joint and amplification chain；
Wherein, the sealed joint includes 5 ' double stranded sections；
Wherein, the amplification chain includes unpaired 5 ' parts, 3 ' double stranded sections and 3 ' T and protruded；
Wherein, the amplification chain includes and the first sequencing primer and the second sequencing primer identical nucleotide sequence；
Wherein, the double stranded section of the sealed joint and the amplification chain has 100% complementarity, and is formed and protruded comprising 3 ' T Described first can connect duplex ends；
Wherein, the double stranded section long enough, to maintain double chain form at a temperature of connection；
Wherein, first target specific primer include can at an annealing temperature specificity be annealed to the target nucleic acid it is described Know the nucleotide sequence of target nucleotide sequences；
Wherein, second target specific primer includes 3 ' and is partly partly annealed to 5 ' parts, described 3 ' containing energy specificity The nucleotide sequence of a part for the known target nucleotide sequences that the amplicon as caused by step (b) is included, the 5 ' portion Point contain with the second sequencing primer identical nucleotide sequence, and second target specific primer is special relative to first target Specific primer is nested；
Wherein, first adapter-primer includes 5 ' the part identical nucleotide sequences with first sequencing primer；And
Wherein, second adapter-primer includes a part of identical nucleotide sequence with first sequencing primer, and phase It is nested for first adapter-primer.
2. the method for claim 1, wherein the sealed joint of the general oligonucleotide pigtail connection further wraps Containing 3 ' unpaired parts, 3 ' the unpaired part does not partly have complementarity with described unpaired the 5 ' of the amplification chain；With And
Wherein, described 3 ' unpaired parts of the sealed joint do not have complementarity with any primer, or do not have with any primer There is uniformity.
3. such as the method any one of claim 1-2, wherein, second adapter-primer passes through at least three nucleotides It is nested relative to first adapter-primer.
4. the method for claim 1, wherein containing identical with first sequencing primer and second sequencing primer Nucleotide sequence the amplification chain part at least partly be contained in it is described amplification chain the unpaired 5 ' part.
5. the method for claim 1, wherein first target specific primer further includes 5 ' sequence label portions Point, 5 ' the sequence label part include have with any other part of any primer it is complementary or not with any primer The nucleotide sequence of any other consistent high GC content in part.
6. the method for claim 1, wherein second adapter-primer is identical with the sequencing primer of total length first.
7. the method for claim 1, wherein the part of the specific target specific primer for being annealed to known target will The specificity annealing at a temperature of 65 DEG C in PCR buffer solutions.
8. the method for claim 1, wherein methods described further comprises the following steps before step (a)：
Mechanical shearing is carried out to the target nucleic acid；
Repair the target nucleic acid experience end；
Make the target nucleic acid experience phosphorylation；
And make the target nucleic acid experience polyadenylation.
9. the method for claim 1, wherein the target nucleic acid is genomic DNA.
10. the method for claim 1, wherein the target nucleic acid is RNA, and methods described further comprises making institute State the first step of target nucleic acid experience reverse transcriptase scheme.
11. the method for claim 1, wherein the reverse transcriptase scheme is including the use of random hexamer.
12. the method for claim 1, wherein known target sequence includes the sequence related to gene rearrangement.
13. method as claimed in claim 12, wherein, the gene rearrangement, which is present in, is selected from what is be made up of following material Nucleic acid in group：
Genomic DNA, RNA and cDNA.
14. method as claimed in claim 12, wherein, the gene rearrangement causes oncogene.
15. method as claimed in claim 14, wherein, the gene rearrangement causes to merge oncogene.
16. the method for claim 1, wherein nucleic acid product is sequenced by PCR sequencing PCR of future generation.
17. method as claimed in claim 16, wherein, the PCR sequencing PCR of future generation includes being selected to be made up of following methods Group in method：
Ion Torrent, SOLiD, 454, extensive parallel signature sequencing, the reversible Dye Terminator thing sequencing of solid phase and DNA receive Rice ball sequencing.
18. method as claimed in claim 16, wherein, the PCR sequencing PCR of future generation is sequenced including Illumina.
19. method as claimed in claim 16, wherein, selected by first sequencing primer and the second sequencing primer compatibility PCR sequencing PCR of future generation.
20. the method for claim 1, wherein methods described is included the independent of the target nucleic acid or the target nucleic acid Part contacts with multigroup first target specific primer and the second target specific primer.
21. the method for claim 1, wherein methods described includes mixing the single reaction comprising the target nucleic acid Thing contacts with multigroup first target specific primer and the second target specific primer.
22. the method as described in claim 20 or 21, wherein, multigroup first target specific primer and the second target-specific Primer specificity is annealed to the known target nucleotide sequences included by different genes.
23. the method as described in claim 20 or 21, wherein, at least two group of first target specific primer and the second target-specific Primer specificity is annealed to the different piece of known target nucleotide sequences.
24. the method as described in claim 20 or 21, wherein, at least two group of first target specific primer and the second target-specific Primer specificity is annealed to the different piece of the individual gene containing known target nucleotide sequences.
25. the method as described in claim 20 or 21, wherein, at least two group of first target specific primer and the second target-specific Primer specificity is annealed to the different extrons of the gene containing known target nucleotide sequences.
26. the method as described in claim 20 or 21, wherein, multiple first target specific primers include the label sequence of identical 5 ' Arrange part.
27. the method for claim 1, wherein the general oligonucleotide pigtail connection further includes barcode section Point.
28. method as claimed in claim 27, wherein, by several samples each with the general widow with unique bar code part Nucleotides pigtail connection contacts；And wherein, the sample is merged after step (a).
29. the method for claim 1, wherein each amplification step includes the PCR that length is -20 circulations of 5 circulations Amplification scheme circulation group.
30. the method for claim 1, wherein the target specific primer and the adapter-primer are designed in 61- Specific their complementary series can be annealed under 72 DEG C of annealing temperature.
31. the method for claim 1, wherein the target specific primer and the adapter-primer are designed to 65 DEG C annealing temperature under can specificity be annealed to their complementary series.
32. the method for claim 1, wherein the target nucleic acid is to be prepared by being derived from the biological sample of subject.
33. the method for claim 1, wherein the target nucleic acid, which is derived from, needs to treat the disease related to hereditary change The subject of disease.
34. method as claimed in claim 33, wherein, the disease is cancer.
35. the method for claim 1, wherein the target nucleic acid is prepared by tumor cell group.
36. the method for claim 1, wherein the target nucleic acid is prepared by tumor biopsies section.
37. method as claimed in claim 34, wherein, the cancer is lung cancer.
38. the method for claim 1, wherein the known target sequence is contained in disease related gene.
39. the method for claim 1, wherein the known target sequence is contained in the gene rearrangement product in sample.
40. method as claimed in claim 39, wherein, the gene rearrangement product is oncogene.
41. the method for claim 1, wherein the known target sequence is included in the group selected from following gene The sequence of gene：
ALK, ROS1 and RET.
42. method as claimed in claim 41, wherein, at least one set of first target specific primer and the second target specific primer Selected from the group being made up of following primer：
SEQ ID NO：5 and SEQ ID NO：6；SEQ ID NO：7 and SEQ ID NO：8；SEQ ID NO：9 and SEQ ID NO： 10；SEQ ID NO：11 and SEQ ID NO：12；SEQ ID NO：13 and SEQ ID NO：14；SEQ ID NO：15 and SEQ ID NO：16；SEQ ID NO：17 and SEQ ID NO：18；SEQ ID NO：19 and SEQ ID NO：20；SEQ ID NO：21 and SEQ ID NO：22；SEQ ID NO：23 and SEQ ID NO：24；SEQ ID NO：25 and SEQ ID NO：26；SEQ ID NO：27 Hes SEQ ID NO：28；SEQ ID NO：29 and SEQ ID NO：30；SEQ ID NO：31 and SEQ ID NO：32；SEQ ID NO： 33 and SEQ ID NO：34；SEQ ID NO：35 and SEQ ID NO：36；And SEQ ID NO：37 and SEQ ID NO：38.
43. method as claimed in claim 41, wherein, the ALK gene rearrangement in the sample obtained from the tumour of subject Presence illustrate the tumour easily by with the group by following material composition therapeutic agent carry out treatment influenceed：
ALK inhibitor and IPI-504.
44. method as claimed in claim 41, wherein, the ALK gene rearrangement in the sample obtained from the tumour of subject Presence illustrate the tumour easily by with the group by following material composition therapeutic agent carry out treatment influenceed：
Gram azoles for Buddhist nun (PF-02341066), AP26113, LDK378, AF802, ASP3026, X-396, GSK-1838705A, CH5424802, NVP-TAE684 and IPI-504.
45. method as claimed in claim 41, wherein, the ROS1 gene rearrangement in the sample obtained from the tumour of subject Presence illustrate the tumour easily by with the group by following material composition therapeutic agent carry out treatment influenceed：
ROS inhibitor, ALK inhibitor and IPI-504.
46. method as claimed in claim 41, wherein, the ROS1 gene rearrangement in the sample obtained from the tumour of subject Presence illustrate the tumour easily by with the group by following material composition therapeutic agent carry out treatment influenceed：
ROS inhibitor, gram azoles are for Buddhist nun (PF-02341066), AP26113, LDK378, AF802, ASP3026, X-396, GSK- 1838705A, CH5424802, NVP-TAE684 and IPI-504.
47. method as claimed in claim 41, wherein, the RET gene rearrangement in the sample obtained from the tumour of subject Presence illustrate the tumour easily by with the group by following material composition therapeutic agent carry out treatment influenceed：
RET inhibitor and withaferin A.
48. method as claimed in claim 41, wherein, the RET gene rearrangement in the sample obtained from the tumour of subject Presence illustrate the tumour easily by with the group by following material composition therapeutic agent carry out treatment influenceed：
SU5416, BAY 43-9006, BAY 73-4506 (Rui Gefeini), ZD6474, NVP-AST487, Sorafenib, RPI- 1st, XL184, ZD6474, Sutent, Imatinib, pazopanib, Axitinib, Mo Tesaini, Gefitinib and liquor-saturated Eggplant element A.
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Families Citing this family (87)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10083273B2 (en) 2005-07-29 2018-09-25 Natera, Inc. System and method for cleaning noisy genetic data and determining chromosome copy number
US9424392B2 (en) 2005-11-26 2016-08-23 Natera, Inc. System and method for cleaning noisy genetic data from target individuals using genetic data from genetically related individuals
US10081839B2 (en) 2005-07-29 2018-09-25 Natera, Inc System and method for cleaning noisy genetic data and determining chromosome copy number
US11111544B2 (en) 2005-07-29 2021-09-07 Natera, Inc. System and method for cleaning noisy genetic data and determining chromosome copy number
US11111543B2 (en) 2005-07-29 2021-09-07 Natera, Inc. System and method for cleaning noisy genetic data and determining chromosome copy number
ES2620431T3 (en) 2008-08-04 2017-06-28 Natera, Inc. Methods for the determination of alleles and ploidy
WO2011041485A1 (en) 2009-09-30 2011-04-07 Gene Security Network, Inc. Methods for non-invasive prenatal ploidy calling
US20190010543A1 (en) 2010-05-18 2019-01-10 Natera, Inc. Methods for simultaneous amplification of target loci
US11939634B2 (en) 2010-05-18 2024-03-26 Natera, Inc. Methods for simultaneous amplification of target loci
US11322224B2 (en) 2010-05-18 2022-05-03 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US11339429B2 (en) 2010-05-18 2022-05-24 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US9677118B2 (en) 2014-04-21 2017-06-13 Natera, Inc. Methods for simultaneous amplification of target loci
US11408031B2 (en) 2010-05-18 2022-08-09 Natera, Inc. Methods for non-invasive prenatal paternity testing
US11326208B2 (en) 2010-05-18 2022-05-10 Natera, Inc. Methods for nested PCR amplification of cell-free DNA
US10316362B2 (en) 2010-05-18 2019-06-11 Natera, Inc. Methods for simultaneous amplification of target loci
US11332785B2 (en) 2010-05-18 2022-05-17 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US11332793B2 (en) 2010-05-18 2022-05-17 Natera, Inc. Methods for simultaneous amplification of target loci
EP2854058A3 (en) 2010-05-18 2015-10-28 Natera, Inc. Methods for non-invasive pre-natal ploidy calling
JP6328934B2 (en) 2010-12-22 2018-05-23 ナテラ， インコーポレイテッド Noninvasive prenatal testing
JP6153874B2 (en) 2011-02-09 2017-06-28 ナテラ， インコーポレイテッド Method for non-invasive prenatal ploidy calls
ES2905448T3 (en) * 2012-05-10 2022-04-08 Massachusetts Gen Hospital Methods for determining a nucleotide sequence
DK2902029T3 (en) 2012-09-25 2018-10-29 Chugai Pharmaceutical Co Ltd RET INHIBITOR
CA2921620C (en) 2013-08-19 2021-01-19 Abbott Molecular Inc. Next-generation sequencing libraries
WO2015048535A1 (en) 2013-09-27 2015-04-02 Natera, Inc. Prenatal diagnostic resting standards
US10262755B2 (en) 2014-04-21 2019-04-16 Natera, Inc. Detecting cancer mutations and aneuploidy in chromosomal segments
US10577655B2 (en) 2013-09-27 2020-03-03 Natera, Inc. Cell free DNA diagnostic testing standards
EP3080303B1 (en) * 2013-12-15 2019-10-30 Academia Sinica Methods for full-length amplification of double-stranded linear nucleic acids of unknown sequences
EP3099820A4 (en) * 2014-01-27 2018-01-03 The General Hospital Corporation Methods of preparing nucleic acids for sequencing
US20150211061A1 (en) * 2014-01-27 2015-07-30 The General Hospital Corporation Methods for determining a nucleotide sequence
CA2938910A1 (en) 2014-02-11 2015-08-20 F. Hoffmann-La Roche Ag Targeted sequencing and uid filtering
EP3561075A1 (en) 2014-04-21 2019-10-30 Natera, Inc. Detecting mutations in tumour biopsies and cell-free samples
AU2015280069B2 (en) 2014-06-23 2021-08-12 The General Hospital Corporation Genomewide unbiased identification of dsbs evaluated by sequencing (guide-seq)
AU2014406026B2 (en) * 2014-09-12 2018-08-23 Mgi Tech Co., Ltd. Isolated oligonucleotide and use thereof in nucleic acid sequencing
US20170281624A1 (en) * 2014-09-13 2017-10-05 Novartis Ag Combination therapies of alk inhibitors
CN105624270B (en) * 2014-10-27 2020-03-24 深圳华大基因股份有限公司 Joint processing method for Small RNA next generation sequencing library building
US20170356918A1 (en) * 2014-12-03 2017-12-14 Ignyta, Inc. Multiplexed immunohistochemistry assays for diagnosis and treatment of cancer
US10876151B2 (en) 2015-04-15 2020-12-29 The General Hospital Corporation LNA-based mutant enrichment next-generation sequencing assays
EP3294906B1 (en) 2015-05-11 2024-07-10 Natera, Inc. Methods for determining ploidy
JP6873921B2 (en) 2015-05-18 2021-05-19 カリウス・インコーポレイテッド Compositions and Methods for Concentrating Nucleic Acid Populations
CA2994601C (en) 2015-08-06 2020-08-25 F. Hoffmann-La Roche Ag Target enrichment by single probe primer extension
WO2017044885A1 (en) * 2015-09-09 2017-03-16 uBiome, Inc. Method and system for microbiome-derived diagnostics and therapeutics for conditions associated with cerebro-craniofacial health
WO2017044843A1 (en) 2015-09-11 2017-03-16 The General Hospital Corporation Full interrogation of nuclease dsbs and sequencing (find-seq)
EP3356526B1 (en) 2015-09-30 2021-08-25 The General Hospital Corporation Comprehensive in vitro reporting of cleavage events by sequencing (circle-seq)
PT3387152T (en) 2015-12-08 2022-04-19 Twinstrand Biosciences Inc Improved adapters, methods, and compositions for duplex sequencing
EP3408406B1 (en) * 2016-01-29 2022-06-15 F. Hoffmann-La Roche AG A novel y-shaped adaptor for nucleic acid sequencing and method of use
JP7071341B2 (en) * 2016-05-17 2022-05-18 ディーネーム－アイティー エンフェー How to identify a sample
EP3464629B1 (en) 2016-06-01 2021-09-08 F. Hoffmann-La Roche AG Immuno-pete
CN106119356B (en) * 2016-06-30 2019-09-24 首度生物科技（苏州）有限公司 A kind of preparation method of molecular label
EP3485034B1 (en) * 2016-07-12 2021-08-18 Kapa Biosystems, Inc. System and method for transposase-mediated amplicon sequencing
CN106282163A (en) * 2016-08-15 2017-01-04 天津诺禾医学检验所有限公司 Construction method based on Ion Torrent order-checking fusion of platforms gene test library and the method for fusion gene detection
AU2017328953B2 (en) 2016-09-15 2023-09-14 Archerdx, Llc Methods of nucleic acid sample preparation for analysis of cell-free DNA
WO2018053362A1 (en) * 2016-09-15 2018-03-22 ArcherDX, Inc. Methods of nucleic acid sample preparation
WO2018067517A1 (en) 2016-10-04 2018-04-12 Natera, Inc. Methods for characterizing copy number variation using proximity-litigation sequencing
EP4198140B1 (en) * 2016-11-02 2024-09-04 ArcherDX, LLC Methods of nucleic acid sample preparation for immune repertoire sequencing
KR101936933B1 (en) * 2016-11-29 2019-01-09 연세대학교 산학협력단 Methods for detecting nucleic acid sequence variations and a device for detecting nucleic acid sequence variations using the same
KR101936934B1 (en) * 2016-11-29 2019-01-09 연세대학교 산학협력단 Methods for detecting nucleic acid sequence variations and a device for detecting nucleic acid sequence variations using the same
US10011870B2 (en) 2016-12-07 2018-07-03 Natera, Inc. Compositions and methods for identifying nucleic acid molecules
EP3585889A1 (en) 2017-02-21 2020-01-01 Natera, Inc. Compositions, methods, and kits for isolating nucleic acids
WO2018162538A1 (en) 2017-03-08 2018-09-13 F. Hoffmann-La Roche Ag Primer extension target enrichment and improvements thereto including simultaneous enrichment of dna and rna
EP3601598B1 (en) 2017-03-23 2022-08-03 University of Washington Methods for targeted nucleic acid sequence enrichment with applications to error corrected nucleic acid sequencing
EP4053294A1 (en) * 2017-03-24 2022-09-07 Life Technologies Corporation Polynucleotide adapters and methods of use thereof
US11505826B2 (en) * 2017-07-12 2022-11-22 Agilent Technologies, Inc. Sequencing method for genomic rearrangement detection
CN109321654A (en) * 2017-07-27 2019-02-12 张巍 Primer sets, kit, library and application for polygene combined detection gynecological tumor
JP6998404B2 (en) * 2017-08-01 2022-02-04 深▲セン▼恒特基因有限公司 Method for enriching and determining the target nucleotide sequence
CA3073448A1 (en) 2017-08-23 2019-02-28 The General Hospital Corporation Engineered crispr-cas9 nucleases with altered pam specificity
WO2019075197A1 (en) 2017-10-11 2019-04-18 The General Hospital Corporation Methods for detecting site-specific and spurious genomic deamination induced by base editing technologies
EP3696275A4 (en) * 2017-10-11 2021-05-26 MGI Tech Co., Ltd. Method for improving loading and stability of nucleic acid on solid support
AU2018366213A1 (en) 2017-11-08 2020-05-14 Twinstrand Biosciences, Inc. Reagents and adapters for nucleic acid sequencing and methods for making such reagents and adapters
JP2021506342A (en) 2017-12-14 2021-02-22 ティーエーアイ ダイアグノスティックス インコーポレイテッドＴａｉ Ｄｉａｇｎｏｓｔｉｃｓ，Ｉｎｃ． Evaluation of Graft Conformity for Transplantation
CN111757934A (en) 2017-12-21 2020-10-09 豪夫迈·罗氏有限公司 Target enrichment by one-way dual probe primer extension
CA3090426A1 (en) 2018-04-14 2019-10-17 Natera, Inc. Methods for cancer detection and monitoring by means of personalized detection of circulating tumor dna
CA3097044A1 (en) 2018-04-17 2019-10-24 The General Hospital Corporation Sensitive in vitro assays for substrate preferences and sites of nucleic acid binding, modifying, and cleaving agents
US11525159B2 (en) 2018-07-03 2022-12-13 Natera, Inc. Methods for detection of donor-derived cell-free DNA
CN110669823B (en) 2018-07-03 2022-05-24 中国医学科学院肿瘤医院 ctDNA library construction and sequencing data analysis method for simultaneously detecting multiple liver cancer common mutations
BR112021000409A2 (en) 2018-07-12 2021-04-06 Twinstrand Biosciences, Inc. METHODS AND REAGENTS TO CHARACTERIZE GENOMIC EDITION, CLONAL EXPANSION AND ASSOCIATED APPLICATIONS
CN109161587A (en) * 2018-09-26 2019-01-08 上海交通大学医学院附属上海儿童医学中心 A method of detection chromosome repeated fragment broken site and location information
AU2019384154A1 (en) * 2018-11-21 2021-06-10 Agilent Technologies, Inc. Methods for targeted nucleic acid library formation
WO2020132316A2 (en) * 2018-12-19 2020-06-25 New England Biolabs, Inc. Target enrichment
US11261479B2 (en) 2019-04-23 2022-03-01 Chapter Diagnostics, Inc. Methods and compositions for enrichment of target nucleic acids
AU2020321991A1 (en) * 2019-08-01 2022-03-03 Twinstrand Biosciences, Inc. Methods and reagents for nucleic acid sequencing and associated applications
WO2021053008A1 (en) * 2019-09-20 2021-03-25 F. Hoffmann-La Roche Ag Immune repertoire profiling by primer extension target enrichment
WO2022125100A1 (en) * 2020-12-10 2022-06-16 Agilent Technologies, Inc. Methods for sequencing polynucleotide fragments from both ends
WO2022146773A1 (en) 2020-12-29 2022-07-07 Nuprobe Usa, Inc. Methods and compositions for sequencing and fusion detection using ligation tail adapters (lta)
WO2022192758A1 (en) * 2021-03-11 2022-09-15 BioSpyder Technologies, Inc. Tempo-span
CN113234799A (en) * 2021-05-11 2021-08-10 赛雷纳（中国）医疗科技有限公司 Method for accurately positioning chromosome deletion/repeated breakpoint
WO2023229999A1 (en) * 2022-05-24 2023-11-30 Accuragen Holdings Limited Compositions and methods for detecting rare sequence variants
GB202210006D0 (en) 2022-07-07 2022-08-24 Achilles Therapeutics Uk Ltd Analysis of T cell samples

Family Cites Families (92)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US4868104A (en) 1985-09-06 1989-09-19 Syntex (U.S.A.) Inc. Homogeneous assay for specific polynucleotides
US6027913A (en) 1988-01-28 2000-02-22 Sommer; Steven S. Nucleic acid amplification with direct sequencing
GB8818020D0 (en) 1988-07-28 1988-09-01 Ici Plc Method for amplification of nucleotide sequences
US6087101A (en) 1990-05-18 2000-07-11 Gruelich; Karl Otto Optical characterization of nucleic acids and oligonucleotides
US5846719A (en) * 1994-10-13 1998-12-08 Lynx Therapeutics, Inc. Oligonucleotide tags for sorting and identification
US5565340A (en) 1995-01-27 1996-10-15 Clontech Laboratories, Inc. Method for suppressing DNA fragment amplification during PCR
JP2001517925A (en) 1995-12-22 2001-10-09 ベーリングウエルケ、アクティエンゲゼルシャフト Homogeneous amplification and detection of nucleic acids
WO1997023646A1 (en) 1995-12-22 1997-07-03 Behringwerke Aktiengesellschaft Detection of differences in nucleic acids
DE69737450T2 (en) * 1996-06-06 2007-11-29 Solexa, Inc., Hayward SEQUENCING BY LIGATION-CODED ADAPTER
US5827658A (en) 1996-08-09 1998-10-27 The United States Of America As Reprsented By The Department Of Health And Human Services Isolation of amplified genes via cDNA subtractive hybridization
US6482590B1 (en) 1996-12-20 2002-11-19 Aventis Behring Gmbh Method for polynucleotide amplification
US6365346B1 (en) 1998-02-18 2002-04-02 Dade Behring Inc. Quantitative determination of nucleic acid amplification products
US6235502B1 (en) 1998-09-18 2001-05-22 Molecular Staging Inc. Methods for selectively isolating DNA using rolling circle amplification
US6200757B1 (en) 1999-01-19 2001-03-13 Dade Behring Inc. Method for controlling the extension of an oligonucleotide
WO2000070095A2 (en) 1999-05-17 2000-11-23 Dade Behring Inc. Homogeneous isothermal amplification and detection of nucleic acids using a template switch oligonucleotide
US6818395B1 (en) 1999-06-28 2004-11-16 California Institute Of Technology Methods and apparatus for analyzing polynucleotide sequences
US6232104B1 (en) 1999-08-17 2001-05-15 Dade Behring Inc. Detection of differences in nucleic acids by inhibition of spontaneous DNA branch migration
DK1218542T3 (en) 1999-09-13 2004-08-02 Nugen Technologies Inc Methods and compositions for linear isothermal amplification of polynucleotide sequences
US7244559B2 (en) 1999-09-16 2007-07-17 454 Life Sciences Corporation Method of sequencing a nucleic acid
WO2001023610A2 (en) 1999-09-29 2001-04-05 Solexa Ltd. Polynucleotide sequencing
US6309836B1 (en) 1999-10-05 2001-10-30 Marek Kwiatkowski Compounds for protecting hydroxyls and methods for their use
WO2001083696A2 (en) 2000-04-28 2001-11-08 Digital Gene Tech Inc Methods for rapid isolation and sequence determination of gene-specific sequences
DE60141087D1 (en) 2000-06-26 2010-03-04 Nugen Technologies Inc METHODS AND COMPOSITIONS FOR TRANSCRIPTION-REPRODUCTIVE MACHINING OF NUCLEIC ACIDS
EP1176212A1 (en) * 2000-07-24 2002-01-30 Centre National de Genotype Method for haplotyping by mass spectrometry
AU2002213096B2 (en) 2000-10-06 2007-03-29 Nugen Technologies, Inc. Methods and probes for detection and/or quantification of nucleic acid sequences
JP2002153271A (en) 2000-11-17 2002-05-28 Jeol Ltd Method for determining base sequence of dna or rna and dna sequencer
EP1427847B1 (en) 2000-12-13 2010-07-28 Nugen Technologies, Inc. Methods and compositions for generation of multiple copies of nucleic acid sequences and methods of detection thereof
AU2005203617A1 (en) 2001-03-09 2005-09-01 Nugen Technologies, Inc Methods and compositions for amplification of RNA sequences
KR20030082535A (en) 2001-03-09 2003-10-22 뉴젠 테크놀로지스 인코포레이티드 Methods and compositions for amplification of rna sequences
US6632611B2 (en) 2001-07-20 2003-10-14 Affymetrix, Inc. Method of target enrichment and amplification
US20030104432A1 (en) 2001-07-27 2003-06-05 The Regents Of The University Of California Methods of amplifying sense strand RNA
EP1488001B1 (en) 2002-03-11 2008-08-20 Nugen Technologies, Inc. Methods for generating double stranded dna comprising a 3' single stranded portion and uses of these complexes for recombination
AU2003222178A1 (en) 2002-03-29 2003-10-13 Nugen Technologies, Inc. Single primer isothermal nucleic acid amplification-enhanced analyte detection and quantification
EP1573056A4 (en) 2002-05-17 2007-11-28 Nugen Technologies Inc Methods for fragmentation, labeling and immobilization of nucleic acids
WO2003100019A2 (en) 2002-05-24 2003-12-04 Invitrogen Corporation Nested pcr employing degradable primers
DK1454992T3 (en) 2003-03-07 2006-10-02 Ist Naz Stud Cura Dei Tumori Anaplastic lymphoma kinase assay, reagents and compositions thereof
US7402386B2 (en) 2003-04-14 2008-07-22 Nugen Technologies, Inc. Global amplification using random priming by a composite primer
US7226720B2 (en) 2003-09-08 2007-06-05 General Electric Company Limited play data storage media and method for limiting access to data thereon
CA2536565A1 (en) 2003-09-10 2005-05-12 Althea Technologies, Inc. Expression profiling using microarrays
US8058032B2 (en) 2003-11-10 2011-11-15 Seegene, Inc. Method for amplifying unknown DNA sequence adjacent to known sequence
US7169560B2 (en) 2003-11-12 2007-01-30 Helicos Biosciences Corporation Short cycle methods for sequencing polynucleotides
US7504509B2 (en) 2003-12-19 2009-03-17 Plexxikon, Inc. Compounds and methods for development of Ret modulators
CA2552007A1 (en) 2003-12-29 2005-07-21 Nugen Technologies, Inc. Methods for analysis of nucleic acid methylation status and methods for fragmentation, labeling and immobilization of nucleic acids
JP3972106B2 (en) 2004-03-03 2007-09-05 大学共同利用機関法人情報・システム研究機構 Genome library production method and genome library produced by the same method
GB0421525D0 (en) 2004-09-28 2004-10-27 Novartis Ag Inhibitors of protein kineses
US20070070349A1 (en) 2005-09-23 2007-03-29 Helicos Biosciences Corporation Optical train and method for TIRF single molecule detection and analysis
US7220549B2 (en) 2004-12-30 2007-05-22 Helicos Biosciences Corporation Stabilizing a nucleic acid for nucleic acid sequencing
EP1929046B1 (en) 2005-09-07 2012-07-11 Nugen Technologies, Inc. Improved nucleic acid amplification procedure
WO2007057652A1 (en) 2005-11-15 2007-05-24 Solexa Limited Method of target enrichment
US7282337B1 (en) 2006-04-14 2007-10-16 Helicos Biosciences Corporation Methods for increasing accuracy of nucleic acid sequencing
ES2400805T3 (en) 2006-05-04 2013-04-12 Seegene, Inc. Method for amplifying an unknown DNA sequence adjacent to a known sequence
WO2007136717A1 (en) 2006-05-16 2007-11-29 Nugen Technologies, Inc. Nucleic acid separation and purification method based on reversible charge interactions
CA2656315A1 (en) 2006-06-30 2008-01-10 Nugen Technologies, Inc. Methods for fragmentation and labeling of nucleic acids
WO2008093098A2 (en) * 2007-02-02 2008-08-07 Illumina Cambridge Limited Methods for indexing samples and sequencing multiple nucleotide templates
WO2009052547A1 (en) 2007-10-22 2009-04-30 Monoquant Pty Ltd A method of dna amplification
WO2009102896A2 (en) 2008-02-12 2009-08-20 Nugen Technologies, Inc. Isothermal nucleic acid amplification methods and compositions
US20090203531A1 (en) 2008-02-12 2009-08-13 Nurith Kurn Method for Archiving and Clonal Expansion
GB2470672B (en) 2008-03-21 2012-09-12 Nugen Technologies Inc Methods of RNA amplification in the presence of DNA
US8029993B2 (en) * 2008-04-30 2011-10-04 Population Genetics Technologies Ltd. Asymmetric adapter library construction
WO2009148617A2 (en) 2008-06-04 2009-12-10 The Salk Institute For Biological Studies Grepseq: an almost inexhaustible, cost-effective, high-throughput protocol for the generation of selector sequences
EP2313091A4 (en) 2008-07-14 2012-04-04 Univ Kingston Pharmaceutical compositions comprising ret inhibitors and methods for the treatment of cancer
WO2010077288A2 (en) 2008-12-09 2010-07-08 The Salk Institute For Biological Studies Methods for identifying differences in alternative splicing between two rna samples
WO2010083046A2 (en) 2009-01-15 2010-07-22 The Salk Institute For Biological Studies Methods for using next generation sequencing to identify 5-methyl cytosines in the genome
US20100286143A1 (en) 2009-04-24 2010-11-11 Dora Dias-Santagata Methods and materials for genetic analysis of tumors
WO2011019964A1 (en) 2009-08-12 2011-02-17 Nugen Technologies, Inc. Methods, compositions, and kits for generating nucleic acid products substantially free of template nucleic acid
EP2475777A4 (en) 2009-09-11 2013-03-06 Nugen Technologies Inc Compositions and methods for whole transcriptome analysis
WO2011053987A1 (en) 2009-11-02 2011-05-05 Nugen Technologies, Inc. Compositions and methods for targeted nucleic acid sequence selection and amplification
WO2011156529A2 (en) 2010-06-08 2011-12-15 Nugen Technologies, Inc. Methods and composition for multiplex sequencing
US20120003657A1 (en) 2010-07-02 2012-01-05 Samuel Myllykangas Targeted sequencing library preparation by genomic dna circularization
CN102345082B (en) 2010-07-29 2017-02-22 比亚迪股份有限公司 Amorphous alloy die casting and heat treatment method thereof
CA2810931C (en) 2010-09-24 2018-04-17 The Board Of Trustees Of The Leland Stanford Junior University Direct capture, amplification and sequencing of target dna using immobilized primers
US20120100549A1 (en) 2010-10-01 2012-04-26 Ibis Biosciences, Inc. Targeted genome amplification methods
WO2012064739A2 (en) 2010-11-08 2012-05-18 The Trustees Of Columbia University In The City Of New York Microbial enrichment primers
JP6328934B2 (en) * 2010-12-22 2018-05-23 ナテラ， インコーポレイテッド Noninvasive prenatal testing
WO2012103154A1 (en) 2011-01-24 2012-08-02 Nugen Technologies, Inc. Stem-loop composite rna-dna adaptor-primers: compositions and methods for library generation, amplification and other downstream manipulations
SG10201605049QA (en) 2011-05-20 2016-07-28 Fluidigm Corp Nucleic acid encoding reactions
EP2714938B1 (en) 2011-05-27 2017-11-15 President and Fellows of Harvard College Methods of amplifying whole genome of a single cell
SG10201510189WA (en) 2011-10-19 2016-01-28 Nugen Technologies Inc Compositions And Methods For Directional Nucleic Acid Amplification And Sequencing
US20130123117A1 (en) 2011-11-16 2013-05-16 The Board Of Trustees Of The Leland Stanford Junior University Capture probe and assay for analysis of fragmented nucleic acids
WO2013112923A1 (en) 2012-01-26 2013-08-01 Nugen Technologies, Inc. Compositions and methods for targeted nucleic acid sequence enrichment and high efficiency library generation
WO2013122826A1 (en) 2012-02-14 2013-08-22 Gnubio, Inc. Cascaded addition of target specific universal adapters to nucleic acids
ES2905448T3 (en) 2012-05-10 2022-04-08 Massachusetts Gen Hospital Methods for determining a nucleotide sequence
EP2861787B1 (en) 2012-06-18 2017-09-20 Nugen Technologies, Inc. Compositions and methods for negative selection of non-desired nucleic acid sequences
US20150011396A1 (en) 2012-07-09 2015-01-08 Benjamin G. Schroeder Methods for creating directional bisulfite-converted nucleic acid libraries for next generation sequencing
WO2014047678A1 (en) 2012-09-25 2014-04-03 Agriculture Victoria Services Pty Ltd Method of producing a normalised nucleic acid library using solid state capture material
EP2971130A4 (en) 2013-03-15 2016-10-05 Nugen Technologies Inc Sequential sequencing
US20140274729A1 (en) 2013-03-15 2014-09-18 Nugen Technologies, Inc. Methods, compositions and kits for generation of stranded rna or dna libraries
JP6525473B2 (en) 2013-11-13 2019-06-05 ニューゲン テクノロジーズ， インコーポレイテッド Compositions and methods for identifying replicate sequencing leads
US9689027B2 (en) 2013-11-15 2017-06-27 The Board Of Trustees Of The Leland Stanford Junior University High efficiency multiplexed nucleic acid capture in a structured microenvironment
AU2017328953B2 (en) 2016-09-15 2023-09-14 Archerdx, Llc Methods of nucleic acid sample preparation for analysis of cell-free DNA
WO2018053362A1 (en) 2016-09-15 2018-03-22 ArcherDX, Inc. Methods of nucleic acid sample preparation
EP4198140B1 (en) 2016-11-02 2024-09-04 ArcherDX, LLC Methods of nucleic acid sample preparation for immune repertoire sequencing

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